Is RINT1 p.Ala459= (c.1377C>T) pathogenic?

RINT1 p.Ala459= (c.1377C>T) is classified Likely benign in RINT1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-08-11). Rare (popmax 0.107%, sas).

How common is RINT1 p.Ala459= (c.1377C>T) in the general population?

RINT1 p.Ala459= (c.1377C>T) is rare (popmax 0.107%, sas) (gnomAD).

RINT1 p.Ala459=

c.1377C>T · rs373723018 · VCV241396

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.107%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.36	GERP 3.2, phastCons 0.99
Overall
CADD	9.564	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.107% South Asian · 97/90,302 alleles

Filtering AF 0.0901% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0836%

Overall 0.0146% 235/1,609,676 alleles · rare exomes 218/1,457,524 · genomes 17/152,152 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.107%	931
Middle Eastern	0.0494%	2,023
Remaining individualsnot grpmax-eligible	0.0145%	6,919
European (non-Finnish)	0.0104%	9,575
Admixed American	0.00505%	19,810

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: RINT1
Protein: p.Ala459=
Coding: c.1377C>T
MANE Select: NM_021930
dbSNP: rs373723018
Type: single nucleotide variant
Location: chr7:105551613 (GRCh38)
Gene constraint: LOEUF 0.931 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 85.97
Residue 459: the rint1/tip20 domain

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

Similar variants

RINT1 p.Ala459Thr Uncertain significance ★★ same residue
RINT1 p.Ala459Gly Uncertain significance ★ ⚠ same residue
RINT1 c.1107+1G>T Likely pathogenic ★★ same type
RINT1 c.1886+5G>A Uncertain significance ★★ same type
RINT1 c.516-3C>T Uncertain significance ★★ same type
RINT1 c.840-12T>A Uncertain significance ★★ same type
RINT1 c.840-3C>G Uncertain significance ★★ same type
RINT1 p.Ala138Thr 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/rint1-p-ala459 (accessed [today's date]).

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