Is SCN8A p.Ser979Phe (c.2936C>T) pathogenic?

SCN8A p.Ser979Phe (c.2936C>T) is classified Pathogenic in SCN8A (ClinVar, Single submitter, 1 submitter; last evaluated 2016-09-13). AlphaMissense: likely pathogenic (0.9855); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with SCN8A p.Ser979Phe (c.2936C>T)?

SCN8A p.Ser979Phe (c.2936C>T) is associated with Inborn genetic diseases (ClinVar).

How common is SCN8A p.Ser979Phe (c.2936C>T) in the general population?

SCN8A p.Ser979Phe (c.2936C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SCN8A p.Ser979Phe (c.2936C>T)?

AlphaMissense predicts likely pathogenic (score 0.9855) — an in-silico prediction, not a clinical call.

SCN8A p.Ser979Phe

c.2936C>T · rs1555226081 · VCV521297

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9855 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9855	likely pathogenic ✓ concordant with ClinVar
REVEL	0.881	moderately pathogenic-leaning
SaProt	LLR -13.08	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.9, phastCons 1
Regional constraint	o/e 0.21	constrained · MANE · 17 kb · p 8.5e-44 · regional, not allelic
Overall
CADD	26.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SCN8A
Protein: p.Ser979Phe
Coding: c.2936C>T
MANE Select: NM_001330260
dbSNP: rs1555226081
Type: single nucleotide variant
Location: chr12:51768899 (GRCh38)
Gene constraint: LOEUF 0.189 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 68.90 · 7 PDB
Residue 979: an α-helix

Full SCN8A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SCN8A p.Arg1620Leu Pathogenic ★★ same condition
SCN8A p.Gly1451Ser Pathogenic ★★ same condition
SCN8A p.Met1760Thr Likely pathogenic ★★ same condition
SCN8A p.Trp1585Ter Likely pathogenic ★★ same condition
SCN8A p.Ala111Thr Uncertain significance ★★ ⚠ same condition
SCN8A p.Ala362Ser Uncertain significance ★★ ⚠ same condition
SCN8A p.Arg1820Gln Uncertain significance ★★ ⚠ same condition
SCN8A p.Arg1841His Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/scn8a-p-ser979phe (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown