RINT1 p.Gln561=
c.1683A>G · rs776730982 · VCV949647
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00503%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -2.5 |
| Overall | ||
| CADD | 3.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00503%
Admixed American · 3/59,662 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00067%
Overall
0.00062%
10/1,612,216 alleles · very rare
exomes 10/1,459,894 · genomes 0/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00503% | 19,887 |
| South Asian | 0.00332% | 30,144 |
| East Asian | 0.00223% | 44,848 |
| European (non-Finnish) | 0.000254% | 393,089 |
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.Gln561=
- Coding
- c.1683A>G
- MANE Select
- NM_021930
- dbSNP
- rs776730982
- Type
- single nucleotide variant
- Location
- chr7:105563744 (GRCh38)
- Gene constraint
- LOEUF 0.931 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.97
- Residue 561
- the rint1/tip20 domain
Similar variants
- RINT1 p.Gln561Lys 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-gln561 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown