Is FIG4 p.Ser11Ala (c.31T>G) pathogenic?

FIG4 p.Ser11Ala (c.31T>G) is classified Uncertain significance in FIG4 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-28). AlphaMissense: likely benign (0.071); Absent from gnomAD v4.1; Associated with amyotrophic lateral sclerosis type 11.

What condition is associated with FIG4 p.Ser11Ala (c.31T>G)?

FIG4 p.Ser11Ala (c.31T>G) is associated with amyotrophic lateral sclerosis type 11, Yunis-Varon syndrome, Charcot-Marie-Tooth disease type 4J (ClinVar).

How common is FIG4 p.Ser11Ala (c.31T>G) in the general population?

FIG4 p.Ser11Ala (c.31T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about FIG4 p.Ser11Ala (c.31T>G)?

AlphaMissense predicts likely benign (score 0.071) — an in-silico prediction, not a clinical call.

FIG4 p.Ser11Ala

c.31T>G · VCV3892150

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.071 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

amyotrophic lateral sclerosis type 11

Computational evidence

Protein change
AlphaMissense	0.071	likely benign
REVEL	0.093	moderately benign-leaning
SaProt	LLR -6.25	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 4	GERP 2.4, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 52 kb · p 0.42 · regional, not allelic
Overall
CADD	22.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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: FIG4
Protein: p.Ser11Ala
Coding: c.31T>G
MANE Select: NM_014845
Type: single nucleotide variant
Location: chr6:109691466 (GRCh38)
Gene constraint: LOEUF 0.966 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.65 · 1 PDB

Full FIG4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

amyotrophic lateral sclerosis type 11 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Yunis-Varon syndrome Charcot-Marie-Tooth disease type 4J bilateral parasagittal parieto-occipital polymicrogyria

Similar variants

FIG4 p.Ser11= Conflicting classifications of pathogenicity ★ same residue
FIG4 c.1040-1G>A Likely pathogenic ★★ same condition
FIG4 c.2376+2T>G Likely pathogenic ★★ same condition
FIG4 c.2459+1G>A Pathogenic ★★ same condition
FIG4 c.877-2A>C Pathogenic/Likely pathogenic ★★ same condition
FIG4 p.Arg183Ter Pathogenic/Likely pathogenic ★★ same condition
FIG4 p.Arg265Ter Pathogenic/Likely pathogenic ★★ same condition
FIG4 p.Arg381Ter Pathogenic ★★ 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/fig4-p-ser11ala (accessed [today's date]).

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