Is EVC2 p.Ala1137Pro (c.3409G>C) pathogenic?

EVC2 p.Ala1137Pro (c.3409G>C) is classified Uncertain significance in EVC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-18). AlphaMissense: likely benign (0.1014); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with EVC2 p.Ala1137Pro (c.3409G>C)?

EVC2 p.Ala1137Pro (c.3409G>C) is associated with Inborn genetic diseases (ClinVar).

How common is EVC2 p.Ala1137Pro (c.3409G>C) in the general population?

EVC2 p.Ala1137Pro (c.3409G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EVC2 p.Ala1137Pro (c.3409G>C)?

AlphaMissense predicts likely benign (score 0.1014) — an in-silico prediction, not a clinical call.

EVC2 p.Ala1137Pro

c.3409G>C · rs773126892 · VCV2255698

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1014 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1014	likely benign
REVEL	0.219	benign-leaning
SaProt	LLR -3.71	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 -0.96	GERP -3.9
Regional constraint	o/e 1.14	unconstrained · MANE · 146 kb · p 1.9e-08 · regional, not allelic
Overall
CADD	14.29	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: EVC2
Protein: p.Ala1137Pro
Coding: c.3409G>C
MANE Select: NM_147127
dbSNP: rs773126892
Type: single nucleotide variant
Location: chr4:5568592 (GRCh38)
Gene constraint: LOEUF 1.092 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 73.33

Full EVC2 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

EVC2 p.Ala1137= Conflicting classifications of pathogenicity ★ same residue
EVC2 p.Ala1137Val Uncertain significance ★ ⚠ same residue
EVC2 p.Gln1089Ter Pathogenic ★★ same condition
EVC2 p.Ala1132Val Uncertain significance ★★ ⚠ same condition
EVC2 p.Ala1150Asp Uncertain significance ★★ ⚠ same condition
EVC2 p.Ala1260Val Uncertain significance ★★ ⚠ same condition
EVC2 p.Ala618Thr Uncertain significance ★★ ⚠ same condition
EVC2 p.Ala703Val 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/evc2-p-ala1137pro (accessed [today's date]).

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