Is COLQ p.Ala338Val (c.1013C>T) pathogenic?

COLQ p.Ala338Val (c.1013C>T) is classified Uncertain significance in COLQ (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-19). AlphaMissense: ambiguous (0.3913); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with COLQ p.Ala338Val (c.1013C>T)?

COLQ p.Ala338Val (c.1013C>T) is associated with Inborn genetic diseases (ClinVar).

How common is COLQ p.Ala338Val (c.1013C>T) in the general population?

COLQ p.Ala338Val (c.1013C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about COLQ p.Ala338Val (c.1013C>T)?

AlphaMissense predicts ambiguous (score 0.3913) — an in-silico prediction, not a clinical call.

COLQ p.Ala338Val

c.1013C>T · rs2470822841 · VCV2336938

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3913 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3913	ambiguous
REVEL	0.632	indeterminate
SaProt	LLR -7.10	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.2, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 70 kb · p 0.34 · 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: COLQ
Protein: p.Ala338Val
Coding: c.1013C>T
MANE Select: NM_005677
dbSNP: rs2470822841
Type: single nucleotide variant
Location: chr3:15456521 (GRCh38)
Gene constraint: LOEUF 0.902 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 55.25 · 2 PDB
Residue 338: a UniProt-annotated variant site (in cms5; pathogenic); a UniProt-annotated variant site (in cms5; pathogenic; impaired anchoring of asymmetric ache to the synaptic basal membrane)

Full COLQ 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

COLQ p.Arg262Cys Uncertain significance ★★ ⚠ same condition
COLQ p.Arg290Lys Uncertain significance ★★ ⚠ same condition
COLQ p.Arg402His Uncertain significance ★★ ⚠ same condition
COLQ p.Arg452His Uncertain significance ★★ ⚠ same condition
COLQ p.Arg45Cys Uncertain significance ★★ ⚠ same condition
COLQ p.Asp447Asn Uncertain significance ★★ ⚠ same condition
COLQ p.Cys52Arg Uncertain significance ★★ ⚠ same condition
COLQ p.Gly147Val 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/colq-p-ala338val (accessed [today's date]).

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