NRAP p.Val939=
c.2817C>T · rs149084999 · VCV4820351
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0415%, 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 4.1 | GERP 0.29, phastCons 1 |
| Overall | ||
| CADD | 6.994 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0415%
African / African-American · 31/74,760 alleles
Filtering AF
0.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0261%
Overall
0.00267%
43/1,613,086 alleles · ultra-rare
exomes 24/1,461,510 · genomes 19/151,576 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0415% | 2,412 |
| Admixed American | 0.005% | 19,983 |
| East Asian | 0.00223% | 44,836 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,478 |
| European (non-Finnish) | 0.000593% | 168,536 |
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
- NRAP
- Protein
- p.Val939=
- Coding
- c.2817C>T
- MANE Select
- NM_198060
- dbSNP
- rs149084999
- Type
- single nucleotide variant
- Location
- chr10:113620661 (GRCh38)
- Gene constraint
- LOEUF 1.045 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.98
Similar variants
- NRAP p.Arg1037Ter Pathogenic/Likely pathogenic ★★ same type
- NRAP p.Trp1033Ter Pathogenic/Likely pathogenic ★★ same type
- NRAP c.360+1G>A Uncertain significance ★★ same type
- NRAP p.Ala29Gly Uncertain significance ★★ ⚠ same type
- NRAP p.Ala571Thr Uncertain significance ★★ same type
- NRAP p.Arg1330Gln Uncertain significance ★★ ⚠ same type
- NRAP p.Arg1559Gln Uncertain significance ★★ ⚠ same type
- NRAP p.Arg428Cys 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/nrap-p-val939 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown