NRAP p.Ser747=
c.2241C>T · rs117385415 · VCV746299
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.24%, 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 -7.8 | GERP -4.2 |
| Overall | ||
| CADD | 1.156 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.24%
East Asian · 557/44,768 alleles
Filtering AF
1.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.12%
Overall
0.101%
1,628/1,608,494 alleles · low-frequency
exomes 1,489/1,456,194 · genomes 139/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.24% | 80 |
| Finnishnot grpmax-eligible | 0.69% | 145 |
| Ashkenazi Jewishnot grpmax-eligible | 0.54% | 185 |
| Remaining individualsnot grpmax-eligible | 0.127% | 789 |
| Middle Eastern | 0.0503% | 1,987 |
| European (non-Finnish) | 0.0328% | 3,050 |
| South Asian | 0.01% | 10,002 |
| African / African-American | 0.00133% | 74,952 |
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.Ser747=
- Coding
- c.2241C>T
- MANE Select
- NM_198060
- dbSNP
- rs117385415
- Type
- single nucleotide variant
- Location
- chr10:113626050 (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-ser747 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown