NRAP p.Asp1328=
c.3984C>T · VCV4909633
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0986%, 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 5.9 | GERP 0.76, phastCons 1 |
| Overall | ||
| CADD | 3.257 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0986%
African / African-American · 74/75,056 alleles
Filtering AF
0.0805%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0738%
Overall
0.00582%
94/1,614,212 alleles · ultra-rare
exomes 47/1,461,888 · genomes 47/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0986% | 1,014 |
| Admixed American | 0.0183% | 5,457 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| South Asian | 0.0011% | 91,080 |
| European (non-Finnish) | 0.000254% | 393,346 |
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.Asp1328=
- Coding
- c.3984C>T
- MANE Select
- NM_198060
- Type
- single nucleotide variant
- Location
- chr10:113604852 (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-asp1328 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown