Is RINT1 p.Ala9= (c.27C>G) pathogenic?

RINT1 p.Ala9= (c.27C>G) is classified Likely benign in RINT1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-09-03). Very rare (popmax 0.00341%, amr).

How common is RINT1 p.Ala9= (c.27C>G) in the general population?

RINT1 p.Ala9= (c.27C>G) is very rare (popmax 0.00341%, amr) (gnomAD).

RINT1 p.Ala9=

c.27C>G · rs1387923124 · VCV1796165

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00341%, amr)

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 0.41	GERP -0.87, phastCons 0.011
Overall
CADD	5.049	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00341% Admixed American · 2/58,592 alleles

Filtering AF 0.000566% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000212%

Overall 0.000125% 2/1,600,108 alleles · very rare exomes 2/1,447,712 · genomes 0/152,396 · joint denominator

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.Ala9=
Coding: c.27C>G
MANE Select: NM_021930
dbSNP: rs1387923124
Type: single nucleotide variant
Location: chr7:105532342 (GRCh38)
Gene constraint: LOEUF 0.931 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 85.97
Residue 9: the 'disordered' region

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

Similar variants

RINT1 p.Ala9Ser Uncertain significance ★ ⚠ same residue
RINT1 p.Ala9Val 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-ala9 (accessed [today's date]).

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