Is ILK p.Asp92= (c.276C>T) pathogenic?

ILK p.Asp92= (c.276C>T) is classified Likely benign in ILK (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-27). Absent from gnomAD v4.1.

How common is ILK p.Asp92= (c.276C>T) in the general population?

ILK p.Asp92= (c.276C>T) is absent from gnomAD v4.1 (gnomAD).

ILK p.Asp92=

c.276C>T · VCV4910474

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.84	GERP 0.73, phastCons 1
Overall
CADD	13.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ILK
Protein: p.Asp92=
Coding: c.276C>T
MANE Select: NM_004517
Type: single nucleotide variant
Location: chr11:6608414 (GRCh38)
Gene constraint: LOEUF 0.798 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.13 · 17 PDB
Residue 92: an α-helix; the 'interaction with lims1' region

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

Similar variants

ILK p.Asp92Asn Uncertain significance ★ ⚠ 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-asp92 (accessed [today's date]).

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