NRAP p.Ser404=
c.1212T>C · rs775208717 · VCV3051372
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0817%, 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 -1.4 | GERP -1.8 |
| Overall | ||
| CADD | 2.223 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0817%
Admixed American · 49/59,942 alleles
Filtering AF
0.0635%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.057%
Overall
0.00352%
55/1,560,676 alleles · ultra-rare
exomes 54/1,408,524 · genomes 1/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0817% | 1,223 |
| East Asian | 0.00448% | 22,326 |
| Remaining individualsnot grpmax-eligible | 0.00329% | 30,366 |
| South Asian | 0.00111% | 90,074 |
| European (non-Finnish) | 8.84e-05% | 1,131,261 |
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.Ser404=
- Coding
- c.1212T>C
- MANE Select
- NM_198060
- dbSNP
- rs775208717
- Type
- single nucleotide variant
- Location
- chr10:113642937 (GRCh38)
- Gene constraint
- LOEUF 1.045 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.98
Disease context
NRAP-related disorder
Similar variants
- 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
- NRAP p.Tyr448Ter 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-ser404 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown