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

ILK p.Ala262Val (c.785C>T) is classified Uncertain significance in ILK (ClinVar, No assertion criteria, 1 submitter; last evaluated 2007-07-31). AlphaMissense: likely benign (0.1074); Very rare (popmax 0.00167%, amr); Associated with Variant of unknown significance.

What condition is associated with ILK p.Ala262Val (c.785C>T)?

ILK p.Ala262Val (c.785C>T) is associated with Variant of unknown significance (ClinVar).

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

ILK p.Ala262Val (c.785C>T) is very rare (popmax 0.00167%, amr) (gnomAD).

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

AlphaMissense predicts likely benign (score 0.1074) — an in-silico prediction, not a clinical call.

ILK p.Ala262Val

c.785C>T · rs387907366 · VCV50371

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1074 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Variant of unknown significance

Computational evidence

Protein change
AlphaMissense	0.1074	likely benign
REVEL	0.589	indeterminate
SaProt	LLR -6.97	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP 1.9, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 6,336 bp · p 0.0056 · regional, not allelic
Overall
CADD	24.9	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

Grpmax group 0.00167% Admixed American · 1/60,012 alleles

Overall 0.000124% 2/1,614,072 alleles · very rare exomes 1/1,461,844 · genomes 1/152,228 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	60,012
European (non-Finnish)	8.47e-05%	1,180,002

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: ILK
Protein: p.Ala262Val
Coding: c.785C>T
MANE Select: NM_004517
dbSNP: rs387907366
Type: single nucleotide variant
Location: chr11:6609568 (GRCh38)
Gene constraint: LOEUF 0.798 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.13 · 17 PDB
Residue 262: a UniProt-annotated variant site (found in a patient with severe dilated cardiomyopathy; uncertain significance); the protein kinase domain; a β-strand

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

Disease context

Variant of unknown significance — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ILK p.Ala262= Likely benign ★★ same residue
ILK p.Ala41Val Uncertain significance ★★ ⚠ same type
ILK p.Arg149Gln Uncertain significance ★★ ⚠ same type
ILK p.Arg161Cys Uncertain significance ★★ ⚠ same type
ILK p.Arg161His Uncertain significance ★★ ⚠ same type
ILK p.Arg334Gln Uncertain significance ★★ ⚠ same type
ILK p.Arg436Gln Uncertain significance ★★ ⚠ same type
ILK p.Arg46Cys 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/ilk-p-ala262val (accessed [today's date]).

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