RINT1 p.Leu485=
c.1453C>T · rs575307435 · VCV1116749
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0313%, eas)
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 1.7 | GERP 1.3, phastCons 0.92 |
| Overall | ||
| CADD | 9.386 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0313%
East Asian · 14/44,716 alleles
Filtering AF
0.0189%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0151%
Overall
0.000996%
16/1,606,512 alleles · ultra-rare
exomes 10/1,454,230 · genomes 6/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0313% | 3,194 |
| Remaining individualsnot grpmax-eligible | 0.00322% | 31,092 |
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.Leu485=
- Coding
- c.1453C>T
- MANE Select
- NM_021930
- dbSNP
- rs575307435
- Type
- single nucleotide variant
- Location
- chr7:105551689 (GRCh38)
- Gene constraint
- LOEUF 0.931 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.97
- Residue 485
- the rint1/tip20 domain
Similar variants
- 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
- RINT1 p.Ala13Val Uncertain significance ★★ ⚠ same type
- RINT1 p.Ala188Ser 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-leu485 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown