Is ILK p.Val96= (c.288G>A) pathogenic?

ILK p.Val96= (c.288G>A) is classified Likely benign in ILK (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-06-09). Very rare (popmax 0.00271%, nfe); Associated with familial hypertrophic cardiomyopathy.

What condition is associated with ILK p.Val96= (c.288G>A)?

ILK p.Val96= (c.288G>A) is associated with familial hypertrophic cardiomyopathy (ClinVar).

How common is ILK p.Val96= (c.288G>A) in the general population?

ILK p.Val96= (c.288G>A) is very rare (popmax 0.00271%, nfe) (gnomAD).

ILK p.Val96=

c.288G>A · rs148059090 · VCV1646085

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00271%, nfe)

Conditions

familial hypertrophic cardiomyopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 3.7	GERP -1.6, phastCons 1
Overall
CADD	9.93	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00271% European (non-Finnish) · 32/1,180,026 alleles

Filtering AF 0.00196% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00168%

Overall 0.00204% 33/1,614,088 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00271%	36,876
Remaining individualsnot grpmax-eligible	0.0016%	62,480

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.Val96=
Coding: c.288G>A
MANE Select: NM_006284 · reported on NM_004517
dbSNP: rs148059090
Type: single nucleotide variant
Location: chr11:6608426 (GRCh38)

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

Disease context

familial hypertrophic cardiomyopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-val96 (accessed [today's date]).

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