NRIP1 p.Val583=
c.1749C>G · rs201255767 · VCV2885158
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.016%, afr)
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 4.5 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 5.547 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.016%
African / African-American · 12/75,024 alleles
Filtering AF
0.0092%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00721%
Overall
0.000743%
12/1,614,070 alleles · ultra-rare
exomes 7/1,461,812 · genomes 5/152,258 · 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
- NRIP1
- Protein
- p.Val583=
- Coding
- c.1749C>G
- MANE Select
- NM_003489
- dbSNP
- rs201255767
- Type
- single nucleotide variant
- Location
- chr21:14966444 (GRCh38)
- Gene constraint
- LOEUF 0.489 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 46.10 · 17 PDB
- Residue 583
- the 'repression domain 2' region
Similar variants
- NRIP1 p.Val583Ile Uncertain significance ★ ⚠ same residue
- NRIP1 p.Ala1096Gly Uncertain significance ★★ ⚠ same type
- NRIP1 p.Ala360Ser Uncertain significance ★★ ⚠ same type
- NRIP1 p.Ala36Pro Uncertain significance ★★ ⚠ same type
- NRIP1 p.Ala792Val Uncertain significance ★★ ⚠ same type
- NRIP1 p.Arg1082Gly Uncertain significance ★★ ⚠ same type
- NRIP1 p.Arg1122Gly Uncertain significance ★★ ⚠ same type
- NRIP1 p.Arg98Trp 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/nrip1-p-val583 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown