HCPCS Level II S3800: Genetic Testing for Amyotrophic Lateral Sclerosis

HCPCS Level II code S3800 describes genetic testing for amyotrophic lateral sclerosis (ALS), a diagnostic molecular test performed to identify genetic variants associated with ALS; the service is a genetic diagnostic test typically performed in an outpatient laboratory or specialized genetic testing facility and billed as a discrete laboratory/genetic testing service.

For related coverage guidance, see recent payer policy updates: Fixed Wing Air Ambulance Transport, Air Ambulance, Ambulance Services (for New Mexico Only).

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HCPCS Level II S3800: Genetic Testing for Amyotrophic Lateral Sclerosis

For related coverage guidance, see recent payer policy updates: Fixed Wing Air Ambulance Transport, Air Ambulance, Ambulance Services (for New Mexico Only).

Customize your policy alerts

Sign up for hcpcs S3800 policy alerts

Get alerted when payer policies referencing S3800 are released or updated.

Monitor payer policy activity

Receive email alerts as soon as relevant payer policies are published or updated.

Clinical & Coding Specifications

Clinical Context

A 48-year-old patient with progressive asymmetric limb weakness, fasciculations, and dysarthria is referred to a neuromuscular clinic for evaluation of suspected amyotrophic lateral sclerosis (ALS). The neurologist documents a detailed history, neurologic exam, and electromyography that support a motor neuron disease process. Genetic counseling is provided and written informed consent is obtained for targeted and panel genetic testing to assess for pathogenic variants associated with familial and sporadic ALS. A peripheral blood sample is collected in the clinic or an outpatient laboratory and sent to a certified molecular diagnostic laboratory for analysis under billing code S3800 (Genetic testing for amyotrophic lateral sclerosis).

The typical workflow includes: pre-test genetic counseling, specimen collection and labeling, shipping to the reference laboratory, laboratory testing (single-gene sequencing and/or multigene panel including common ALS genes such as C9orf72, SOD1, TARDBP, FUS), reporting of results with interpretation, and post-test counseling to discuss pathogenic, likely pathogenic, variant of uncertain significance, or negative results. Results may impact family counseling, cascade testing of relatives, clinical prognosis, and eligibility for gene-targeted clinical trials. The typical site of service is an outpatient neurology clinic or an ambulatory phlebotomy/laboratory collection center. Frequently involved providers include neurologists, genetic counselors, and clinical laboratory specialists.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`88181`	Cytogenetic analysis, interpretation and report, first cell; limited	May be performed when cytogenetic assessment is required in differential diagnosis or concurrent testing for other neuromuscular disorders.
`81320`	SMN1 (survival motor neuron gene) analysis; gene-level testing (eg, deletion/duplication)	Performed in the differential diagnosis of motor neuron disorders; sometimes ordered to exclude spinal muscular atrophy in certain presentations.
`81327`	C9orf72 (chromosome 9 open reading frame 72) (eg, repeat expansion analysis)	Commonly ordered specifically for ALS testing to detect pathogenic hexanucleotide repeat expansions and often included in ALS genetic panels billed under `S3800`.
`81479`	Unlisted molecular pathology procedure	Used for novel or complex molecular testing not described by existing CPT codes when additional or customized assays are required alongside standard ALS testing.
`96372`	Therapeutic, prophylactic, or diagnostic injection (subcutaneous or intramuscular)	May be billed if intravenous or intramuscular medications are administered during a clinic visit where specimen collection or counseling occurs (contextual ancillary service).

Related Modifiers

7 rows

Modifier	Description	When to Use
22	Modifier –22 (Increased Procedural Services) is used when a reported procedure is substantially more extensive than normally required. The CPT Manual and CMS state it may be appended only when the…	- When to use: Append modifier -22 to a procedural CPT code when the service performed is substantially more extensive than the usual service described by that code — i.e., the procedure required…
26	Modifier 26 (Professional Component) identifies and bills only the professional portion of a split service — the physician’s interpretation, report, and medical judgment — when the technical…	- Use CPT Modifier -26 when you are billing only the professional component (PC) of a split‑bill eligible service—i.e., you performed the physician interpretation, medical judgment and prepared a…
52	Modifier ‑52 (Reduced Services) indicates that a service or procedure was partially reduced or omitted at the provider’s discretion, allowing reporting of the basic procedure number with a qualifier…	- Use modifier -52 when a physician or qualified health professional electively reduces or omits part of a procedure or service (for example, performing fewer required views or omitting a portion of…
53	Modifier 53 (Discontinued Procedure) signals that a surgical or diagnostic service was begun by the physician but terminated because of extenuating circumstances that threatened the patient’s…	- Use modifier -53 when a physician/qualified healthcare professional has started a surgical or diagnostic procedure (e.g., anesthesia administered, incision or scope insertion) and then discontinues…
62	Modifier 62 indicates that two surgeons function as co‑surgeons, each performing distinct parts of the same primary surgical procedure. It is appended to the primary procedure code (and any…	- Use modifier -62 when two surgeons act as co‑surgeons (both primary surgeons) on a single definitive primary procedure, each performing distinct parts of the same surgical procedure (append -62 to…
80	CPT® Modifier 80 (Assistant Surgeon) is appended to a surgical CPT code when a physician (MD or DO) provides full, continuous assistance throughout the operative procedure. It is intended only for…	- Use CPT Modifier -80 when a physician (MD or DO) serves as an assistant surgeon and provides full, continuous assistance throughout the entire operative procedure; append -80 to the surgical CPT…
82	Modifier 82 is appended to a surgical CPT code to indicate that an attending physician acted as an assistant because a qualified resident surgeon was unavailable. In teaching hospitals it documents…	- When to use: Append modifier 82 in teaching-hospital settings to indicate a physician served as an assistant surgeon because a qualified resident surgeon was unavailable (includes situations where…

Related Provider Taxonomies

8 rows

Taxonomy Code	Specialty	Notes
2084P0800X	Psychiatry Physician	A Psychiatrist specializes in the prevention, diagnosis, and treatment of mental disorders, emotional disorders, psychotic disorders, mood disorders, …
363L00000X	Nurse Practitioner	(1) A registered nurse provider with a graduate degree in nursing prepared for advanced practice involving independent and interdependent decision mak…
207Q00000X	Family Medicine Physician	Family Medicine is the medical specialty which is concerned with the total health care of the individual and the family. It is the specialty in breadt…
367A00000X	Advanced Practice Midwife	Advanced practice midwifery encompasses the independent provision of care during pregnancy, childbirth, and the postpartum period; sexual and reproduc…
364S00000X	Clinical Nurse Specialist	A registered nurse who, through a graduate degree program in nursing, or through a formal post-basic education program or continuing education courses…
2080P0006X	Developmental - Behavioral Pediatrics Physician	A developmental-behavioral specialist is a pediatrician with special training and experience who aims to foster understanding and promotion of optimal…
2080A0000X	Pediatric Adolescent Medicine Physician	A pediatrician who specializes in adolescent medicine is a multi-disciplinary healthcare specialist trained in the unique physical, psychological and …
2251G0304X	Geriatric Physical Therapist	A licensed physical therapist, including but not limited to an individual who is a Board Certified Specialist in Geriatric Physical Therapy, who has d…

Related ICD-10-CM Codes

26 rows

ICD-10-CM Code	Description
F82	Specific developmental disorder of motor function
G12.20	Motor neuron disease, unspecified
G12.21	Amyotrophic lateral sclerosis
G12.22	Progressive bulbar palsy
G31.84	Mild cognitive impairment of uncertain or unknown etiology
G31.9	Degenerative disease of nervous system, unspecified
M54.2	Cervicalgia
M62.81	Muscle weakness (generalized)
R13.10	Dysphagia, unspecified
R13.11	Dysphagia, oral phase

Showing 1–10 of 26

Related Payer Policy Updates

Specialty: Emergency & Medical Transportation1 / 3

10 rows

Policy	Payer	Effective Date
Fixed Wing Air Ambulance Transport	Cigna	2026-08-15
Air Ambulance	Ambetter Georgia	2026-08-01
Ambulance Services (for New Mexico Only)	UnitedHealthcare	2026-08-01
Ambulance Services (for Tennessee Only)	UnitedHealthcare	2026-08-01
Clinical Policy: Air Ambulance	Ambetter Nevada	2026-08-01
Clinical Policy: Air Ambulance	Centene	2026-08-01
Air Ambulance	Centene	2026-08-01
Clinical Policy: Air Ambulance	Arizona Complete Health	2026-08-01
Ambulance Transport	Providence Health Plan	2026-07-01
Air Ambulance Transport	eocco	2026-07-01

HCPCS Level II S2152: Solid Organ Procurement and Transplantation

HCPCS-LEVEL-II-S2266-INDUCED-ABORTION-29-TO-31-WEEKS

HCPCS Level II S2266: Induced Abortion, 29 to 31 Weeks

HCPCS-LEVEL-II-S3630-EOSINOPHIL-COUNT-BLOOD-DIRECT

HCPCS Level II S3630: Eosinophil Count, Blood, Direct

HCPCS-LEVEL-II-S4017-INCOMPLETE-ART-CYCLE-CANCELLED-PRIOR-TO-STIMULATION

HCPCS Level II S4017: Incomplete Cycle — Cancelled Prior to Stimulation

HCPCS-LEVEL-II-S8055-ULTRASOUND-GUIDANCE-MULTIFETAL-REDUCTION-TC

HCPCS Level II S8055: Ultrasound Guidance for Multifetal Pregnancy Reduction

HCPCS-LEVEL-II-S8940-EQUESTRIAN-HIPPOTHERAPY-PER-SESSION

HCPCS Level II S8940: Equestrian/Hippotherapy, Per Session

HCPCS-LEVEL-II-S9024-PARANASAL-SINUS-ULTRASOUND

HCPCS Level II S9024: Paranasal Sinus Ultrasound

HCPCS-LEVEL-II-S9366-HOME-TPN-1-2L-PER-DAY-HOME-INFUSION

HCPCS Level II S9366: Home Infusion TPN, 1–2 L/day

HCPCS-LEVEL-II-S9446-GROUP-PATIENT-EDUCATION-NON-PHYSICIAN

HCPCS S9446: Patient Education, Non-Physician Provider, Group, Per Session

HCPCS-LEVEL-II-S9451-EXERCISE-CLASS-NON-PHYSICIAN-SESSION

HCPCS S9451: Exercise Classes, Non-Physician Provider, Per Session

Showing 1–10 of 532

Frequently Asked Questions

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Aug 11, 2026.Maintains the CPT code set's official descriptions and guidelines, licensed from the American Medical Association, used as the definitional source for CPT codes on this page.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's quarterly release of HCPCS Level II codes and short/long descriptors, the source for HCPCS code definitions and update history.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's complete ICD-10-CM diagnosis code list, used to cross-reference diagnosis codes associated with this procedure or service.

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Trek Health ingests and normalizes Transparency in Coverage data and payer policy updates to give provider organizations a clear view of how commercial reimbursement behaves across markets, payers, and services. Our platform transforms raw payer disclosures into structured intelligence that supports contract evaluation, payer negotiations, and service line strategy. By combining market benchmarks with ongoing policy visibility, Trek helps teams identify variability, risk, and opportunity in commercial reimbursement. The result is faster insight, stronger negotiating positions, and more informed financial decisions.

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Clinical & Coding Specifications

Clinical Context

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`88181`	Cytogenetic analysis, interpretation and report, first cell; limited	May be performed when cytogenetic assessment is required in differential diagnosis or concurrent testing for other neuromuscular disorders.
`81320`	SMN1 (survival motor neuron gene) analysis; gene-level testing (eg, deletion/duplication)	Performed in the differential diagnosis of motor neuron disorders; sometimes ordered to exclude spinal muscular atrophy in certain presentations.
`81327`	C9orf72 (chromosome 9 open reading frame 72) (eg, repeat expansion analysis)	Commonly ordered specifically for ALS testing to detect pathogenic hexanucleotide repeat expansions and often included in ALS genetic panels billed under `S3800`.
`81479`	Unlisted molecular pathology procedure	Used for novel or complex molecular testing not described by existing CPT codes when additional or customized assays are required alongside standard ALS testing.
`96372`	Therapeutic, prophylactic, or diagnostic injection (subcutaneous or intramuscular)	May be billed if intravenous or intramuscular medications are administered during a clinic visit where specimen collection or counseling occurs (contextual ancillary service).

Related Modifiers

7 rows

Modifier	Description	When to Use
22	Modifier –22 (Increased Procedural Services) is used when a reported procedure is substantially more extensive than normally required. The CPT Manual and CMS state it may be appended only when the…	- When to use: Append modifier -22 to a procedural CPT code when the service performed is substantially more extensive than the usual service described by that code — i.e., the procedure required…
26	Modifier 26 (Professional Component) identifies and bills only the professional portion of a split service — the physician’s interpretation, report, and medical judgment — when the technical…	- Use CPT Modifier -26 when you are billing only the professional component (PC) of a split‑bill eligible service—i.e., you performed the physician interpretation, medical judgment and prepared a…
52	Modifier ‑52 (Reduced Services) indicates that a service or procedure was partially reduced or omitted at the provider’s discretion, allowing reporting of the basic procedure number with a qualifier…	- Use modifier -52 when a physician or qualified health professional electively reduces or omits part of a procedure or service (for example, performing fewer required views or omitting a portion of…
53	Modifier 53 (Discontinued Procedure) signals that a surgical or diagnostic service was begun by the physician but terminated because of extenuating circumstances that threatened the patient’s…	- Use modifier -53 when a physician/qualified healthcare professional has started a surgical or diagnostic procedure (e.g., anesthesia administered, incision or scope insertion) and then discontinues…
62	Modifier 62 indicates that two surgeons function as co‑surgeons, each performing distinct parts of the same primary surgical procedure. It is appended to the primary procedure code (and any…	- Use modifier -62 when two surgeons act as co‑surgeons (both primary surgeons) on a single definitive primary procedure, each performing distinct parts of the same surgical procedure (append -62 to…
80	CPT® Modifier 80 (Assistant Surgeon) is appended to a surgical CPT code when a physician (MD or DO) provides full, continuous assistance throughout the operative procedure. It is intended only for…	- Use CPT Modifier -80 when a physician (MD or DO) serves as an assistant surgeon and provides full, continuous assistance throughout the entire operative procedure; append -80 to the surgical CPT…
82	Modifier 82 is appended to a surgical CPT code to indicate that an attending physician acted as an assistant because a qualified resident surgeon was unavailable. In teaching hospitals it documents…	- When to use: Append modifier 82 in teaching-hospital settings to indicate a physician served as an assistant surgeon because a qualified resident surgeon was unavailable (includes situations where…

Related Provider Taxonomies

8 rows

Taxonomy Code	Specialty	Notes
2084P0800X	Psychiatry Physician	A Psychiatrist specializes in the prevention, diagnosis, and treatment of mental disorders, emotional disorders, psychotic disorders, mood disorders, …
363L00000X	Nurse Practitioner	(1) A registered nurse provider with a graduate degree in nursing prepared for advanced practice involving independent and interdependent decision mak…
207Q00000X	Family Medicine Physician	Family Medicine is the medical specialty which is concerned with the total health care of the individual and the family. It is the specialty in breadt…
367A00000X	Advanced Practice Midwife	Advanced practice midwifery encompasses the independent provision of care during pregnancy, childbirth, and the postpartum period; sexual and reproduc…
364S00000X	Clinical Nurse Specialist	A registered nurse who, through a graduate degree program in nursing, or through a formal post-basic education program or continuing education courses…
2080P0006X	Developmental - Behavioral Pediatrics Physician	A developmental-behavioral specialist is a pediatrician with special training and experience who aims to foster understanding and promotion of optimal…
2080A0000X	Pediatric Adolescent Medicine Physician	A pediatrician who specializes in adolescent medicine is a multi-disciplinary healthcare specialist trained in the unique physical, psychological and …
2251G0304X	Geriatric Physical Therapist	A licensed physical therapist, including but not limited to an individual who is a Board Certified Specialist in Geriatric Physical Therapy, who has d…

Related ICD-10-CM Codes

26 rows

ICD-10-CM Code	Description
F82	Specific developmental disorder of motor function
G12.20	Motor neuron disease, unspecified
G12.21	Amyotrophic lateral sclerosis
G12.22	Progressive bulbar palsy
G31.84	Mild cognitive impairment of uncertain or unknown etiology
G31.9	Degenerative disease of nervous system, unspecified
M54.2	Cervicalgia
M62.81	Muscle weakness (generalized)
R13.10	Dysphagia, unspecified
R13.11	Dysphagia, oral phase

Showing 1–10 of 26

Related Payer Policy Updates

Specialty: Emergency & Medical Transportation1 / 3

10 rows

Policy	Payer	Effective Date
Fixed Wing Air Ambulance Transport	Cigna	2026-08-15
Air Ambulance	Ambetter Georgia	2026-08-01
Ambulance Services (for New Mexico Only)	UnitedHealthcare	2026-08-01
Ambulance Services (for Tennessee Only)	UnitedHealthcare	2026-08-01
Clinical Policy: Air Ambulance	Ambetter Nevada	2026-08-01
Clinical Policy: Air Ambulance	Centene	2026-08-01
Air Ambulance	Centene	2026-08-01
Clinical Policy: Air Ambulance	Arizona Complete Health	2026-08-01
Ambulance Transport	Providence Health Plan	2026-07-01
Air Ambulance Transport	eocco	2026-07-01

HCPCS Level II S2152: Solid Organ Procurement and Transplantation

HCPCS-LEVEL-II-S2266-INDUCED-ABORTION-29-TO-31-WEEKS

HCPCS Level II S2266: Induced Abortion, 29 to 31 Weeks

HCPCS-LEVEL-II-S3630-EOSINOPHIL-COUNT-BLOOD-DIRECT

HCPCS Level II S3630: Eosinophil Count, Blood, Direct

HCPCS-LEVEL-II-S4017-INCOMPLETE-ART-CYCLE-CANCELLED-PRIOR-TO-STIMULATION

HCPCS Level II S4017: Incomplete Cycle — Cancelled Prior to Stimulation

HCPCS-LEVEL-II-S8055-ULTRASOUND-GUIDANCE-MULTIFETAL-REDUCTION-TC

HCPCS Level II S8055: Ultrasound Guidance for Multifetal Pregnancy Reduction

HCPCS-LEVEL-II-S8940-EQUESTRIAN-HIPPOTHERAPY-PER-SESSION

HCPCS Level II S8940: Equestrian/Hippotherapy, Per Session

HCPCS-LEVEL-II-S9024-PARANASAL-SINUS-ULTRASOUND

HCPCS Level II S9024: Paranasal Sinus Ultrasound

HCPCS-LEVEL-II-S9366-HOME-TPN-1-2L-PER-DAY-HOME-INFUSION

HCPCS Level II S9366: Home Infusion TPN, 1–2 L/day

HCPCS-LEVEL-II-S9446-GROUP-PATIENT-EDUCATION-NON-PHYSICIAN

HCPCS S9446: Patient Education, Non-Physician Provider, Group, Per Session

HCPCS-LEVEL-II-S9451-EXERCISE-CLASS-NON-PHYSICIAN-SESSION

HCPCS S9451: Exercise Classes, Non-Physician Provider, Per Session

Showing 1–10 of 532

Frequently Asked Questions

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Aug 11, 2026.Maintains the CPT code set's official descriptions and guidelines, licensed from the American Medical Association, used as the definitional source for CPT codes on this page.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's quarterly release of HCPCS Level II codes and short/long descriptors, the source for HCPCS code definitions and update history.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's complete ICD-10-CM diagnosis code list, used to cross-reference diagnosis codes associated with this procedure or service.

Published by

Trek Health powers OpenPayer with a leading commercial payer intelligence platform, seamlessly converting fragmented payer data into actionable insights for provider organizations.

OpenPayer

HCPCS Level II S3800: Genetic Testing for Amyotrophic Lateral Sclerosis

Sign up for hcpcs S3800 policy alerts

OpenPayer

HCPCS Level II S3800: Genetic Testing for Amyotrophic Lateral Sclerosis

Sign up for hcpcs S3800 policy alerts

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related ICD-10-CM Codes

Related Payer Policy Updates

Related Codes

References

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related ICD-10-CM Codes

Related Payer Policy Updates

Related Codes

References

HCPCS Level II S3800: Genetic Testing for Amyotrophic Lateral Sclerosis

Sign up for hcpcs S3800 policy alerts

HCPCS Level II S3800: Genetic Testing for Amyotrophic Lateral Sclerosis

Sign up for hcpcs S3800 policy alerts

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related ICD-10-CM Codes

Related Payer Policy Updates

Related Codes

What does HCPCS Level II code S3800 represent?

What is the usual clinical workflow when S3800 testing is ordered and how are results used?

Which related CPT codes or services should be considered alongside S3800?

For which diagnoses is S3800 commonly used?

Which payers are mentioned for S3800 and does the page provide reimbursement rates?

References

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related ICD-10-CM Codes

Related Payer Policy Updates

Related Codes

What does HCPCS Level II code S3800 represent?

What is the usual clinical workflow when S3800 testing is ordered and how are results used?

Which related CPT codes or services should be considered alongside S3800?

For which diagnoses is S3800 commonly used?

Which payers are mentioned for S3800 and does the page provide reimbursement rates?

References