RINT1 p.Ile539=
c.1617T>A · rs1203373982 · VCV1153173
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000508%, nfe)
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 1.1 | GERP 0.004, phastCons 1 |
| Overall | ||
| CADD | 8.974 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000508%
European (non-Finnish) · 6/1,180,008 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000372%
6/1,614,088 alleles · very rare
exomes 6/1,461,774 · genomes 0/152,314 · 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.Ile539=
- Coding
- c.1617T>A
- MANE Select
- NM_021930
- dbSNP
- rs1203373982
- Type
- single nucleotide variant
- Location
- chr7:105555173 (GRCh38)
- Gene constraint
- LOEUF 0.931 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.97
- Residue 539
- the rint1/tip20 domain
Similar variants
- RINT1 p.Ile539Val 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
- RINT1 p.Ala13Val 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-ile539 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown