Is ANKRD6 p.Ala262Val (c.785C>T) pathogenic?

ANKRD6 p.Ala262Val (c.785C>T) is classified Uncertain significance in ANKRD6 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-16). AlphaMissense: likely benign (0.3372); Very rare (popmax 0.00017%, nfe).

How common is ANKRD6 p.Ala262Val (c.785C>T) in the general population?

ANKRD6 p.Ala262Val (c.785C>T) is very rare (popmax 0.00017%, nfe) (gnomAD).

What do computational predictors say about ANKRD6 p.Ala262Val (c.785C>T)?

AlphaMissense predicts likely benign (score 0.3372) — an in-silico prediction, not a clinical call.

ANKRD6 p.Ala262Val

c.785C>T · rs367712968 · VCV2604166

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3372 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00017%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3372	likely benign
REVEL	0.21	benign-leaning
SaProt	LLR -11.85	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.7, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 64 kb · p 0.065 · regional, not allelic
Overall
CADD	28.2	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

Grpmax group 0.00017% European (non-Finnish) · 2/1,179,902 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000124% 2/1,614,064 alleles · very rare exomes 2/1,461,700 · genomes 0/152,364 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ANKRD6
Protein: p.Ala262Val
Coding: c.785C>T
MANE Select: NM_001242809
dbSNP: rs367712968
Type: single nucleotide variant
Location: chr6:89618024 (GRCh38)
Gene constraint: LOEUF 0.869 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.82

Full ANKRD6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ANKRD6 p.Ala140Val Uncertain significance ★ ⚠ same type
ANKRD6 p.Ala173Glu Uncertain significance ★ same type
ANKRD6 p.Ala182Val Uncertain significance ★ ⚠ same type
ANKRD6 p.Ala206Gly Uncertain significance ★ ⚠ same type
ANKRD6 p.Ala206Thr Uncertain significance ★ ⚠ same type
ANKRD6 p.Ala229Thr Uncertain significance ★ ⚠ same type
ANKRD6 p.Ala390Ser Uncertain significance ★ same type
ANKRD6 p.Ala390Val Uncertain significance ★ ⚠ same type

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/ankrd6-p-ala262val (accessed [today's date]).

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