NRIP1 p.Pro1041=
c.3123C>G · rs373749896 · VCV2189315
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.109%, 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 5.2 | GERP 0.24, phastCons 1 |
| Overall | ||
| CADD | 7.906 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.109%
East Asian · 49/44,874 alleles
Filtering AF
0.0848%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0762%
Overall
0.0031%
50/1,613,672 alleles · rare
exomes 42/1,461,528 · genomes 8/152,144 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.109% | 916 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,500 |
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.Pro1041=
- Coding
- c.3123C>G
- MANE Select
- NM_003489
- dbSNP
- rs373749896
- Type
- single nucleotide variant
- Location
- chr21:14965070 (GRCh38)
- Gene constraint
- LOEUF 0.489 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 46.10 · 17 PDB
- Residue 1041
- the 'interaction with znf366' region
Similar variants
- NRIP1 p.Pro1041Thr 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-pro1041 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown