Is RINT1 p.Lys510= (c.1530G>A) pathogenic?

RINT1 p.Lys510= (c.1530G>A) is classified Likely benign in RINT1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-05). Very rare (popmax 0.00833%, amr).

How common is RINT1 p.Lys510= (c.1530G>A) in the general population?

RINT1 p.Lys510= (c.1530G>A) is very rare (popmax 0.00833%, amr) (gnomAD).

RINT1 p.Lys510=

c.1530G>A · rs777841156 · VCV416381

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00833%, 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 2.2	GERP 0.69, phastCons 1
Overall
CADD	7.424	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00833% Admixed American · 5/59,992 alleles

Filtering AF 0.00323% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00207%

Overall 0.0013% 21/1,613,846 alleles · very rare exomes 16/1,461,720 · genomes 5/152,126 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00833%	11,998
Remaining individualsnot grpmax-eligible	0.0016%	62,476
European (non-Finnish)	0.00127%	78,665

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.Lys510=
Coding: c.1530G>A
MANE Select: NM_021930
dbSNP: rs777841156
Type: single nucleotide variant
Location: chr7:105555086 (GRCh38)
Gene constraint: LOEUF 0.931 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 85.97
Residue 510: the rint1/tip20 domain

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

Similar variants

RINT1 p.Lys510Arg Uncertain significance ★ ⚠ same residue
RINT1 p.Lys510Gln Uncertain significance ★ ⚠ same residue
RINT1 p.Lys510Glu Uncertain significance ★ ⚠ same residue
RINT1 p.Lys510Ter 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

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-lys510 (accessed [today's date]).

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