Is CHIC2 p.Pro160Gln (c.479C>A) pathogenic?

CHIC2 p.Pro160Gln (c.479C>A) is classified Uncertain significance in CHIC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-26). AlphaMissense: ambiguous (0.4161); No allele count reported in gnomAD v4.1 (AN 1,606,710).

How common is CHIC2 p.Pro160Gln (c.479C>A) in the general population?

CHIC2 p.Pro160Gln (c.479C>A) is no allele count reported in gnomAD v4.1 (AN 1,606,710) (gnomAD).

What do computational predictors say about CHIC2 p.Pro160Gln (c.479C>A)?

AlphaMissense predicts ambiguous (score 0.4161) — an in-silico prediction, not a clinical call.

CHIC2 p.Pro160Gln

c.479C>A · VCV4653386

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4161 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,606,710)

Computational evidence

Protein change
AlphaMissense	0.4161	ambiguous
REVEL	0.342	indeterminate
SaProt	LLR -6.76	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.9	GERP 2.9, phastCons 1
Regional constraint	o/e 0.72	unconstrained · MANE · 54 kb · p 8.1e-05 · regional, not allelic
Overall
CADD	22.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,606,710). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHIC2
Protein: p.Pro160Gln
Coding: c.479C>A
MANE Select: NM_012110
Type: single nucleotide variant
Location: chr4:54010114 (GRCh38)
Gene constraint: LOEUF 0.766 · pLI 0.18 (gnomAD)
Structure: AlphaFold pLDDT 84.67 · 1 PDB

Full CHIC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHIC2 p.Arg163Gln Uncertain significance ★ ⚠ same type
CHIC2 p.Arg16Gln Uncertain significance ★ ⚠ same type
CHIC2 p.Glu20Ala Uncertain significance ★ ⚠ same type
CHIC2 p.Ile151Met Uncertain significance ★ ⚠ same type
CHIC2 p.Leu75Val Uncertain significance ★ ⚠ same type
CHIC2 p.Lys109Arg Uncertain significance ★ ⚠ same type
CHIC2 p.Ser137Arg Uncertain significance ★ ⚠ same type
CHIC2 p.Thr39Ile 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/chic2-p-pro160gln (accessed [today's date]).

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