Is ILK p.Phe344= (c.1032C>T) pathogenic?

ILK p.Phe344= (c.1032C>T) is classified Likely benign in ILK (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-22). Very rare (popmax 0.00161%, nfe).

How common is ILK p.Phe344= (c.1032C>T) in the general population?

ILK p.Phe344= (c.1032C>T) is very rare (popmax 0.00161%, nfe) (gnomAD).

ILK p.Phe344=

c.1032C>T · rs1358304642 · VCV1771553

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00161%, nfe)

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 4.9	GERP 1.8, phastCons 1
Overall
CADD	19.87	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00161% European (non-Finnish) · 19/1,180,044 alleles

Filtering AF 0.00103% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00083%

Overall 0.00137% 20/1,461,850 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00161%	62,108
Remaining individualsnot grpmax-eligible	0.0016%	62,512

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.Phe344=
Coding: c.1032C>T
MANE Select: NM_004517
dbSNP: rs1358304642
Type: single nucleotide variant
Location: chr11:6609989 (GRCh38)
Gene constraint: LOEUF 0.798 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.13 · 17 PDB
Residue 344: the protein kinase domain

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

Similar variants

ILK p.Phe344Tyr 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-phe344 (accessed [today's date]).

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