Is RINT1 p.Ser129= (c.387C>T) pathogenic?

RINT1 p.Ser129= (c.387C>T) is classified Likely benign in RINT1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-30). Ultra-rare (popmax 0.0144%, nfe).

How common is RINT1 p.Ser129= (c.387C>T) in the general population?

RINT1 p.Ser129= (c.387C>T) is ultra-rare (popmax 0.0144%, nfe) (gnomAD).

RINT1 p.Ser129=

c.387C>T · rs769363586 · VCV416395

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0144%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Overall
CADD	5.37	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0144% European (non-Finnish) · 170/1,180,028 alleles

Filtering AF 0.0126% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0119%

Overall 0.0117% 189/1,614,006 alleles · ultra-rare exomes 174/1,461,876 · genomes 15/152,130 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0144%	6,941
Remaining individualsnot grpmax-eligible	0.0144%	6,943
Finnishnot grpmax-eligible	0.0109%	9,147
East Asian	0.00445%	22,449
South Asian	0.0011%	91,080

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.Ser129=
Coding: c.387C>T
MANE Select: NM_021930
dbSNP: rs769363586
Type: single nucleotide variant
Location: chr7:105542521 (GRCh38)
Gene constraint: LOEUF 0.931 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 85.97

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

Similar variants

RINT1 p.Ser129Arg Uncertain significance ★ ⚠ same residue
RINT1 p.Ser129Gly Uncertain significance ★ ⚠ same residue
RINT1 p.Ser129Thr 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

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-ser129 (accessed [today's date]).

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