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F78.A1 ICD-10-CM Code: SYNGAP1-related intellectual disability

F78.A1 is not a CMS-HCC payment code. MEAT criteria · RAF Calculator · free HCC coding tools

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Code lookupF78.A1

FY 2026 Apr update / Mental, Behavioral and Neurodevelopmental disorders (F01-F99) / Intellectual Disabilities (F70-F79)

F78.A1

Billable / SpecificICD-10-CMOfficial ICD-10-CMCodebook guidance

SYNGAP1-related intellectual disability

A genetic developmental condition caused by mutations in the SYNGAP1 gene, resulting in intellectual disability of varying severity along with potential behavioral, neurological, and developmental challenges.

Buddy the Bee presenting code insight

Buddy Insight

SYNGAP1-related intellectual disability is a specific genetic form caused by mutations in the SYNGAP1 gene, which plays a critical role in synaptic function and neurodevelopment.

OverviewRisk ModelsCode BookDocumentationAuditNotesEdition comparison

CMS-HCC V28

N/A

—

Not mapped

CMS-HCC V24

Historical

Historical

Not used for CY2026 payment

ACA/HHS

N/A

—

Not mapped

ESRD/PACE

N/A

—

Not mapped

RXHCC

HCC 147

Code-level coefficient reference

Code Book Path

Official
F78Other intellectual disabilitiesF78.AOther genetic related intellectual disabilitiesF78.A1SYNGAP1-related intellectual disability

Inclusion Terms

Official

No inclusion terms are included in this display for F78.A1. Check the code and parent instructions in the Code Book.

Excludes 2

Official
  • symptoms, signs and abnormal clinical laboratory findings, not elsewhere classified (R00-R99)Inherited from F01-F99

Related Codes

Official
F78.A9Other genetic related intellectual disability

Includes

Official
  • disorders of psychological developmentInherited from F01-F99

Excludes 1

Official
  • borderline intellectual functioning, IQ above 70 to 84 (R41.83)Inherited from F70-F79

Code First

Official
  • any associated physical or developmental disordersInherited from F70-F79

Use Additional

Official

No Use Additional Code instructions are included in this display for F78.A1. Check the code and parent instructions in the Code Book.

Code Also

Official
  • , if applicable, any associated:
  • autism spectrum disorder (F84.0)
  • autistic disorder (F84.0)
  • encephalopathy (G93.4-)
  • epilepsy and recurrent seizures (G40.-)
  • other pervasive developmental disorders (F84.8)
  • pervasive developmental disorder, NOS (F84.9)

Buddy Documentation Tip

HCC Buddy guidance
Genetic testing results confirming a pathogenic or likely pathogenic variant in the SYNGAP1 gene
Provider documentation linking the intellectual disability to the SYNGAP1 mutation
Documentation of the severity of intellectual disability and associated features (epilepsy, behavioral issues)
Current treatment plan including anti-epileptic medications if applicable

MEAT Support

HCC Buddy guidance
Genetic testing results confirming a pathogenic or likely pathogenic variant in the SYNGAP1 gene
Provider documentation linking the intellectual disability to the SYNGAP1 mutation
Documentation of the severity of intellectual disability and associated features (epilepsy, behavioral issues)
Current treatment plan including anti-epileptic medications if applicable

Audit Caution

HCC Buddy guidance
Using generic intellectual disability codes (F70-F73, F79) when SYNGAP1 mutation has been confirmed — use the specific genetic code
Failing to also code comorbid epilepsy (G40.x) and autism spectrum disorder (F84.x) when present
Not updating the record when genetic testing results become available after an initial unspecified intellectual disability diagnosis
Coding F78.A9 (other genetic) when SYNGAP1 has been specifically identified

Common Mistakes

HCC Buddy guidance
F78.A9 — Other genetic related intellectual disability; use F78.A1 specifically when SYNGAP1 is identified
F71 — Moderate intellectual disabilities; when the genetic etiology is known (SYNGAP1), use F78.A1 rather than severity-only codes
G40.x — Epilepsy codes; epilepsy associated with SYNGAP1 should be coded separately in addition to F78.A1
F84.0 — Autistic disorder; autism features in SYNGAP1 are coded additionally if they meet diagnostic criteria

Current with CMS: FY2026 ICD-10-CM Apr 1 update (effective Apr 1 – Sep 30, 2026) · CMS-HCC V28, 100% phased in for payment year 2026. FY2027 code set already staged for October 1, 2026. How HCC Buddy stays current →

Is F78.A1 an HCC code?

F78.A1 is not in the CMS-HCC V28 or V24 community payment model. F78.A1 has a separate mapping under the Part D RxHCC model (HCC 147 (Moderate Intellectual Disability/Developmental Disorder)); the applicable result needs member context.

Code
F78.A1
Description
SYNGAP1-related intellectual disability
HCC (V28)
No CMS-HCC V28 mapping
RAF reference coefficient
—
Billable
Yes
Payment year
2026

HCC Category Mapping

RxHCCHCC 147, Moderate Intellectual Disability/Developmental Disorder
Not separately weighted

These are source-labeled model coefficients, not member totals. A category may still be removed by hierarchy or model cleanup rules. Weights are not directly comparable across models: CMS-HCC V28 and V24 use Community, Non-Dual, Aged; ESRD uses the dialysis continuing-enrollee model; RxHCC is the Part D continuing-enrollee, non-low-income, aged weight (a larger scale than CMS-HCC). ACA/HHS has no single weight — it varies by metal level. Actual per-patient RAF contribution depends on member context, hierarchy and cleanup rules, interactions, and the model year used by the payer. V28 is the CMS-HCC model phased in over payment years 2024–2026; V24 remains available for historical review.

Work F78.A1 in the Code Book — tabular path, V28 RAF reference, and MEAT checklist →

MEAT review for F78.A1

For F78.A1, confirm that the documentation supports the diagnosis and meets the applicable coding, encounter, program and payer requirements. MEAT (Monitor, Evaluate, Assess, or Treat) is a review mnemonic, not a universal CMS coding rule.

  • MMonitor: signs, symptoms, disease progression, or lab trending documented in the note
  • EEvaluate: test results, medication response, or physical findings reviewed by the provider
  • AAssess: explicit mention in the assessment or plan with acknowledgment of status
  • TTreat: medication, referral, procedure, therapy, or counseling tied to the diagnosis

Coder workflow notes

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What This Code Means

F78.A1 is the ICD-10-CM diagnosis code for syngap1-related intellectual disability. A genetic developmental condition caused by mutations in the SYNGAP1 gene, resulting in intellectual disability of varying severity along with potential behavioral, neurological, and developmental challenges. F78.A1 sits in the ICD-10-CM chapter for mental, behavioral and neurodevelopmental disorders (f01-f99), within the section covering intellectual disabilities (f70-f79).

F78.A1 has no mapping under the CMS-HCC V28 or V24 community payment models. F78.A1 has a separate mapping under the Part D RxHCC model (HCC 147 (Moderate Intellectual Disability/Developmental Disorder)); the applicable result needs member context. Do not assign V28 risk adjustment value from this page; verify the applicable model and payment year before using this code for risk adjustment.

Document genetic testing results confirming SYNGAP1 mutation in the medical record.

HCC Buddy maintains structured V28 and V24 mapping, source-labeled coefficient references, and MEAT documentation criteria for F78.A1 sourced directly from the CMS-HCC risk adjustment model files and the CMS ICD-10-CM code set.

Coding Tips

  • •Document genetic testing results confirming SYNGAP1 mutation in the medical record
  • •Specify the severity level of intellectual disability (mild, moderate, severe, or profound) if determined

Clinical Significance

SYNGAP1-related intellectual disability is a specific genetic form caused by mutations in the SYNGAP1 gene, which plays a critical role in synaptic function and neurodevelopment. It typically presents with moderate to severe intellectual disability, epilepsy (often treatment-resistant), and autism spectrum features. This is a relatively newly recognized genetic etiology with an ICD-10-CM code that allows for precise tracking of this rare condition for research and treatment development purposes.

Documentation Requirements

  • ✓Genetic testing results confirming a pathogenic or likely pathogenic variant in the SYNGAP1 gene
  • ✓Provider documentation linking the intellectual disability to the SYNGAP1 mutation
  • ✓Documentation of the severity of intellectual disability and associated features (epilepsy, behavioral issues)
  • ✓Current treatment plan including anti-epileptic medications if applicable
  • ✓Genetic counseling documentation if relevant

Code Also

  • , if applicable, any associated:
  • autism spectrum disorder (F84.0)
  • autistic disorder (F84.0)
  • encephalopathy (G93.4-)
  • epilepsy and recurrent seizures (G40.-)
  • other pervasive developmental disorders (F84.8)
  • pervasive developmental disorder, NOS (F84.9)

Commonly Confused Codes

  • •F78.A9: Other genetic related intellectual disability; use F78.A1 specifically when SYNGAP1 is identified
  • •F71: Moderate intellectual disabilities; when the genetic etiology is known (SYNGAP1), use F78.A1 rather than severity-only codes
  • •G40.x: Epilepsy codes; epilepsy associated with SYNGAP1 should be coded separately in addition to F78.A1
  • •F84.0: Autistic disorder; autism features in SYNGAP1 are coded additionally if they meet diagnostic criteria

Child Codes

F78.A1SYNGAP1-related intellectual disability
F78.A9Other genetic related intellectual disability

Code Hierarchy

└F78Other intellectual disabilities└F78.AOther genetic related intellectual disabilities└F78.A1SYNGAP1-related intellectual disability
└F78.A1SYNGAP1-related intellectual disability

F78.A1 code history

Code setChange
FY2022 (effective Oct 1, 2021)Added to the code set

Source: official CMS ICD-10-CM order and addenda files, FY2016 through FY2027.

Also searched as

  • F78 A1
  • F78A1

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