Is RIN1 p.Arg342His (c.1025G>A) pathogenic?

RIN1 p.Arg342His (c.1025G>A) is classified Uncertain significance in RIN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-05). AlphaMissense: likely benign (0.0846); Ultra-rare (popmax 0.0615%, afr).

How common is RIN1 p.Arg342His (c.1025G>A) in the general population?

RIN1 p.Arg342His (c.1025G>A) is ultra-rare (popmax 0.0615%, afr) (gnomAD).

What do computational predictors say about RIN1 p.Arg342His (c.1025G>A)?

AlphaMissense predicts likely benign (score 0.0846) — an in-silico prediction, not a clinical call.

RIN1 p.Arg342His

c.1025G>A · VCV3433487

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0846 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0615%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0846	likely benign
REVEL	0.022	moderately benign-leaning
SaProt	LLR -8.09	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.53	GERP -1.1, phastCons 0.072
Regional constraint	o/e 0.98	unconstrained · MANE · 4,123 bp · p 0.45 · regional, not allelic
Overall
CADD	15.96	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.0615% African / African-American · 45/73,180 alleles

Filtering AF 0.0472% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0421%

Overall 0.00407% 63/1,548,760 alleles · ultra-rare exomes 32/1,396,440 · genomes 31/152,320 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0615%	1,626
Admixed American	0.00782%	12,789
Remaining individualsnot grpmax-eligible	0.00501%	19,973
East Asian	0.00244%	41,002
South Asian	0.00237%	42,118
European (non-Finnish)	0.000698%	143,341

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: RIN1
Protein: p.Arg342His
Coding: c.1025G>A
MANE Select: NM_004292
Type: single nucleotide variant
Location: chr11:66334774 (GRCh38)
Gene constraint: LOEUF 1.22 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.78
Residue 342: the 'ras and 14-3-3 protein binding region' region; the 'disordered' region

Full RIN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RIN1 p.Ala690= Benign ★★ same type
RIN1 p.Gly737= Benign ★★ same type
RIN1 p.Thr643= Benign/Likely benign ★★ same type
RIN1 p.Val700Ile Benign ★★ same type
RIN1 p.Ala111Thr Uncertain significance ★ ⚠ same type
RIN1 p.Ala168Thr Uncertain significance ★ ⚠ same type
RIN1 p.Ala221Ser Uncertain significance ★ ⚠ same type
RIN1 p.Ala31Val 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/rin1-p-arg342his (accessed [today's date]).

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