NHS p.Ala32Pro
c.94G>C · rs1465452744 · VCV2303703
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000232%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.039 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.061 | GERP -1.8 |
| Regional constraint | o/e 0.79 | unconstrained · MANE · 357 kb · p 1.3e-14 · regional, not allelic |
| Overall | ||
| CADD | 10.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000232%
European (non-Finnish) · 2/862,987 alleles
Filtering AF
3.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.4e-05%
Overall
0.000177%
2/1,129,870 alleles · very rare
exomes 1/1,017,672 · genomes 1/112,198 · joint denominator
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
- NHS
- Protein
- p.Ala32Pro
- Coding
- c.94G>C
- MANE Select
- NM_001291867
- dbSNP
- rs1465452744
- Type
- single nucleotide variant
- Location
- chrX:17375851 (GRCh38)
- Structure
- AlphaFold pLDDT 43.65
- Residue 32
- the 'wave homology domain (whd)' region; the 'disordered' region
Similar variants
- NHS p.Arg162Cys Uncertain significance ★★ same condition
- NHS p.Arg17Trp Uncertain significance ★★ same condition
- NHS p.Arg204His Uncertain significance ★★ same condition
- NHS p.Arg231Gln Uncertain significance ★★ same condition
- NHS p.Arg698Trp Uncertain significance ★★ same condition
- NHS p.Asp1284His Uncertain significance ★★ same condition
- NHS p.Cys1373Tyr Uncertain significance ★★ same condition
- NHS p.Glu101Ala Uncertain significance ★★ 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/nhs-p-ala32pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown