Is RINT1 p.Arg629Ser (c.1887A>T) pathogenic?

RINT1 p.Arg629Ser (c.1887A>T) is classified Uncertain significance in RINT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-05). AlphaMissense: likely pathogenic (0.8111); Absent from gnomAD v4.1.

How common is RINT1 p.Arg629Ser (c.1887A>T) in the general population?

RINT1 p.Arg629Ser (c.1887A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about RINT1 p.Arg629Ser (c.1887A>T)?

AlphaMissense predicts likely pathogenic (score 0.8111) — an in-silico prediction, not a clinical call.

RINT1 p.Arg629Ser

c.1887A>T · rs2485181920 · VCV1781990

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8111 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.8111	likely pathogenic
REVEL	0.28	benign-leaning
SaProt	LLR -4.72	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.12	GERP -5.7, phastCons 0.083
Regional constraint	o/e 0.96	unconstrained · MANE · 35 kb · p 0.28 · regional, not allelic
Overall
CADD	20.4	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: RINT1
Protein: p.Arg629Ser
Coding: c.1887A>T
MANE Select: NM_021930
dbSNP: rs2485181920
Type: single nucleotide variant
Location: chr7:105565277 (GRCh38)

Full RINT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/rint1-p-arg629ser (accessed [today's date]).

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