Is ITGA6 p.Val808Met (c.2422G>A) pathogenic?

ITGA6 p.Val808Met (c.2422G>A) is classified Uncertain significance in ITGA6 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-23). AlphaMissense: ambiguous (0.4926); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ITGA6 p.Val808Met (c.2422G>A)?

ITGA6 p.Val808Met (c.2422G>A) is associated with Inborn genetic diseases (ClinVar).

How common is ITGA6 p.Val808Met (c.2422G>A) in the general population?

ITGA6 p.Val808Met (c.2422G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ITGA6 p.Val808Met (c.2422G>A)?

AlphaMissense predicts ambiguous (score 0.4926) — an in-silico prediction, not a clinical call.

ITGA6 p.Val808Met

c.2422G>A · VCV4039961

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4926 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4926	ambiguous
REVEL	0.353	indeterminate
SaProt	LLR -8.16	tolerated
Splicing
SpliceAI	Δ0.38	acceptor loss at this position · masked 0 · deltas
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 22 kb · p 0.00022 · regional, not allelic
Overall
CADD	27.7	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM V847M vs ClinVar V808M) — verify the residue.

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: ITGA6
Protein: p.Val808Met
Coding: c.2422G>A
MANE Select: NM_000210
Type: single nucleotide variant
Location: chr2:172488145 (GRCh38)
Gene constraint: LOEUF 0.52 · pLI 0.69 (gnomAD)
Structure: AlphaFold pLDDT 80.05 · 2 PDB

Full ITGA6 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

ITGA6 p.Ala1024Thr Uncertain significance ★★ ⚠ same condition
ITGA6 p.Ala491Val Uncertain significance ★★ ⚠ same condition
ITGA6 p.Ala90Thr Uncertain significance ★★ ⚠ same condition
ITGA6 p.Arg19Trp Uncertain significance ★★ ⚠ same condition
ITGA6 p.Arg484His Uncertain significance ★★ ⚠ same condition
ITGA6 p.Arg578His Uncertain significance ★★ ⚠ same condition
ITGA6 p.Arg902Gln Uncertain significance ★★ ⚠ same condition
ITGA6 p.Arg913Gly 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/itga6-p-val808met (accessed [today's date]).

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