Is CHN1 p.Ile369Ser (c.1106T>G) pathogenic?

CHN1 p.Ile369Ser (c.1106T>G) is classified Pathogenic in CHN1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-12). AlphaMissense: likely benign (0.0762); Absent from gnomAD v4.1; Associated with autosomal dominant Robinow syndrome 2.

What condition is associated with CHN1 p.Ile369Ser (c.1106T>G)?

CHN1 p.Ile369Ser (c.1106T>G) is associated with autosomal dominant Robinow syndrome 2 (ClinVar).

How common is CHN1 p.Ile369Ser (c.1106T>G) in the general population?

CHN1 p.Ile369Ser (c.1106T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CHN1 p.Ile369Ser (c.1106T>G)?

AlphaMissense predicts likely benign (score 0.0762) — an in-silico prediction, not a clinical call.

CHN1 p.Ile369Ser

c.1106T>G · rs1684730153 · VCV974781

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0762 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

autosomal dominant Robinow syndrome 2

Computational evidence

Protein change
AlphaMissense	0.0762	likely benign ⚠ discordant with ClinVar
REVEL	0.1	moderately benign-leaning
SaProt	LLR -9.31	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.21	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 7	GERP 0.69, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 24 kb · p 0.00014 · regional, not allelic
Overall
CADD	24.9	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

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: CHN1
Protein: p.Ile369Ser
Coding: c.1106T>G
MANE Select: NM_001822
dbSNP: rs1684730153
Type: single nucleotide variant
Location: chr2:174801809 (GRCh38)
Gene constraint: LOEUF 0.79 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.41 · 2 PDB
Residue 369: the rho-gap domain

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

Disease context

autosomal dominant Robinow syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHN1 c.-160C>G Uncertain significance ★★ same type
CHN1 c.-74C>T Uncertain significance ★★ same type
CHN1 p.Ala27Gly Uncertain significance ★★ ⚠ same type
CHN1 p.Asp440Gly Uncertain significance ★★ ⚠ same type
CHN1 p.Lys260Asn Uncertain significance ★★ ⚠ same type
CHN1 p.Thr167Ile Uncertain significance ★★ ⚠ same type
CHN1 p.Val65Met Uncertain significance ★★ ⚠ same type
CHN1 c.886+15G>A Benign ★★ 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/chn1-p-ile369ser (accessed [today's date]).

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