Is ILK p.Ile60= (c.180C>T) pathogenic?

ILK p.Ile60= (c.180C>T) is classified Likely benign in ILK (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-18). Very rare (popmax 0.0011%, sas); Associated with familial hypertrophic cardiomyopathy.

What condition is associated with ILK p.Ile60= (c.180C>T)?

ILK p.Ile60= (c.180C>T) is associated with familial hypertrophic cardiomyopathy (ClinVar).

How common is ILK p.Ile60= (c.180C>T) in the general population?

ILK p.Ile60= (c.180C>T) is very rare (popmax 0.0011%, sas) (gnomAD).

ILK p.Ile60=

c.180C>T · VCV4721707

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

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 1.1	GERP 0.73, phastCons 1
Overall
CADD	11.23	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,070 alleles

Overall 6.84e-05% 1/1,461,886 alleles · very rare

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.Ile60=
Coding: c.180C>T
MANE Select: NM_006284 · reported on NM_004517
Type: single nucleotide variant
Location: chr11:6608136 (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-ile60 (accessed [today's date]).

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