NRAP p.Val207=
c.621G>A · rs1157202473 · VCV3040581
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
Conditions
1
NRAP-related disorder
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 | GERP 2.3, phastCons 1 |
| Overall | ||
| CADD | 9.717 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/59,992 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000372%
6/1,613,352 alleles · very rare
exomes 4/1,461,230 · genomes 2/152,122 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 19,997 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,231 |
| European (non-Finnish) | 8.48e-05% | 1,179,468 |
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.Val207=
- Coding
- c.621G>A
- MANE Select
- NM_198060
- dbSNP
- rs1157202473
- Type
- single nucleotide variant
- Location
- chr10:113651857 (GRCh38)
- Gene constraint
- LOEUF 1.045 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.98
Disease context
NRAP-related disorder
Similar variants
- NRAP p.Val207fs Likely pathogenic same residue
- NRAP p.Arg1037Ter Pathogenic/Likely pathogenic ★★ same condition
- NRAP p.Trp1033Ter Pathogenic/Likely pathogenic ★★ same condition
- NRAP c.1843-2A>G Likely pathogenic ★ same condition
- NRAP p.Gln24His Pathogenic ★ same condition
- NRAP p.Gln607Ter Likely pathogenic ★ same condition
- NRAP p.Glu1256Ter Likely pathogenic ★ same condition
- NRAP p.Tyr127Ter Likely pathogenic ★ same condition
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-val207 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown