Is SOX11 p.Ser287Cys (c.860C>G) pathogenic?

SOX11 p.Ser287Cys (c.860C>G) is classified Uncertain significance in SOX11 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-08-14). AlphaMissense: likely benign (0.2773); Absent from gnomAD v4.1; Associated with SOX11-related disorder.

What condition is associated with SOX11 p.Ser287Cys (c.860C>G)?

SOX11 p.Ser287Cys (c.860C>G) is associated with SOX11-related disorder (ClinVar).

How common is SOX11 p.Ser287Cys (c.860C>G) in the general population?

SOX11 p.Ser287Cys (c.860C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SOX11 p.Ser287Cys (c.860C>G)?

AlphaMissense predicts likely benign (score 0.2773) — an in-silico prediction, not a clinical call.

SOX11 p.Ser287Cys

c.860C>G · VCV3350084

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2773 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

SOX11-related disorder

Computational evidence

Protein change
AlphaMissense	0.2773	likely benign
REVEL	0.554	indeterminate
SaProt	LLR -10.93	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.7	GERP -0.6, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 774 bp · p 1 · regional, not allelic
Overall
CADD	26.5	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: SOX11
Protein: p.Ser287Cys
Coding: c.860C>G
MANE Select: NM_003108
Type: single nucleotide variant
Location: chr2:5693581 (GRCh38)
Gene constraint: LOEUF 1.148 · pLI 0.09 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 58.44 · 4 PDB
Residue 287: a UniProt-annotated variant site (in iddmoh); the 'disordered' region

Full SOX11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

SOX11-related disorder

Similar variants

SOX11 p.Ser287Thr Uncertain significance ★★ ⚠ same residue
SOX11 p.Ser287Phe Uncertain significance ★ ⚠ same residue
SOX11 p.Pro52Gln Likely pathogenic ★ same condition
SOX11 p.Ser71Pro Likely pathogenic ★ same condition
SOX11 p.Trp41Ter Likely pathogenic ★ same condition
SOX11 p.Ser354Asn Conflicting classifications of pathogenicity ★ ⚠ same condition
SOX11 p.Lys50Glu Likely pathogenic same condition
SOX11 p.Ser335Cys 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/sox11-p-ser287cys (accessed [today's date]).

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