Is ILK p.Ser396= (c.1188C>A) pathogenic?

ILK p.Ser396= (c.1188C>A) is classified Likely benign in ILK (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-22). Ultra-rare (popmax 0.0147%, afr); Associated with familial hypertrophic cardiomyopathy.

What condition is associated with ILK p.Ser396= (c.1188C>A)?

ILK p.Ser396= (c.1188C>A) is associated with familial hypertrophic cardiomyopathy (ClinVar).

How common is ILK p.Ser396= (c.1188C>A) in the general population?

ILK p.Ser396= (c.1188C>A) is ultra-rare (popmax 0.0147%, afr) (gnomAD).

ILK p.Ser396=

c.1188C>A · rs769331209 · VCV1122732

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0147%, afr)

Conditions

familial hypertrophic cardiomyopathy

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

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 1.4	GERP 0.88, phastCons 1
Overall
CADD	9.435	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0147% African / African-American · 11/74,896 alleles

Filtering AF 0.00816% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00633%

Overall 0.0013% 21/1,614,016 alleles · ultra-rare exomes 19/1,461,870 · genomes 2/152,146 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0147%	6,809
Remaining individualsnot grpmax-eligible	0.0016%	62,488
European (non-Finnish)	0.000763%	131,116

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.Ser396=
Coding: c.1188C>A
MANE Select: NM_004517
dbSNP: rs769331209
Type: single nucleotide variant
Location: chr11:6610257 (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-ser396 (accessed [today's date]).

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