Is CHN1 p.Asp320His (c.958G>C) pathogenic?

CHN1 p.Asp320His (c.958G>C) is classified Uncertain significance in CHN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-21). AlphaMissense: likely pathogenic (0.9937); Very rare (popmax 0.00221%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CHN1 p.Asp320His (c.958G>C)?

CHN1 p.Asp320His (c.958G>C) is associated with Inborn genetic diseases (ClinVar).

How common is CHN1 p.Asp320His (c.958G>C) in the general population?

CHN1 p.Asp320His (c.958G>C) is very rare (popmax 0.00221%, nfe) (gnomAD).

What do computational predictors say about CHN1 p.Asp320His (c.958G>C)?

AlphaMissense predicts likely pathogenic (score 0.9937) — an in-silico prediction, not a clinical call.

CHN1 p.Asp320His

c.958G>C · VCV3833094

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9937 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00221%, nfe)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9937	likely pathogenic
REVEL	0.727	pathogenic-leaning
SaProt	LLR -13.21	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 24 kb · p 0.00014 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00221% European (non-Finnish) · 26/1,176,350 alleles

Filtering AF 0.00154% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00131%

Overall 0.00185% 27/1,456,704 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00221%	45,244
Remaining individualsnot grpmax-eligible	0.0016%	62,314

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: CHN1
Protein: p.Asp320His
Coding: c.958G>C
MANE Select: NM_001822
Type: single nucleotide variant
Location: chr2:174811517 (GRCh38)
Gene constraint: LOEUF 0.79 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.41 · 2 PDB
Residue 320: the rho-gap domain; an α-helix

Full CHN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHN1 p.Ala27Gly Uncertain significance ★★ ⚠ same condition
CHN1 p.Asp440Gly Uncertain significance ★★ ⚠ same condition
CHN1 p.Arg295Ile Uncertain significance ★ same condition
CHN1 p.Arg321Thr Conflicting classifications of pathogenicity ★ ⚠ same condition
CHN1 p.Arg428Lys Uncertain significance ★ ⚠ same condition
CHN1 p.Arg73Trp Uncertain significance ★ ⚠ same condition
CHN1 p.Asn207Ser Uncertain significance ★ ⚠ same condition
CHN1 p.Asn337Thr Uncertain significance ★ ⚠ same condition

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/chn1-p-asp320his (accessed [today's date]).

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