Is ILK p.Phe287= (c.861C>T) pathogenic?

ILK p.Phe287= (c.861C>T) is classified Likely benign in ILK (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-19). Ultra-rare (popmax 0.0133%, amr); Associated with familial hypertrophic cardiomyopathy.

What condition is associated with ILK p.Phe287= (c.861C>T)?

ILK p.Phe287= (c.861C>T) is associated with familial hypertrophic cardiomyopathy (ClinVar).

How common is ILK p.Phe287= (c.861C>T) in the general population?

ILK p.Phe287= (c.861C>T) is ultra-rare (popmax 0.0133%, amr) (gnomAD).

ILK p.Phe287=

c.861C>T · rs779980137 · VCV1099321

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, amr)

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 -7.1	GERP -3.6
Overall
CADD	0.874	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0133% Admixed American · 8/60,010 alleles

Filtering AF 0.00661% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00482%

Overall 0.0018% 29/1,614,070 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0133%	7,501
African / African-American	0.00801%	12,487
Remaining individualsnot grpmax-eligible	0.0016%	62,482
European (non-Finnish)	0.0011%	90,772
South Asian	0.0011%	91,084

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.Phe287=
Coding: c.861C>T
MANE Select: NM_006284 · reported on NM_004517
dbSNP: rs779980137
Type: single nucleotide variant
Location: chr11:6609728 (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-phe287 (accessed [today's date]).

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