NHS p.Pro655=
c.1965T>G · rs151009077 · VCV96633
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.187%, afr)
Conditions
2
Inborn genetic diseases
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 -0.26 | GERP -5.8, phastCons 0.47 |
| Overall | ||
| CADD | 1.347 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.187%
African / African-American · 107/57,183 alleles
Filtering AF
0.158%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.148%
Overall
0.0119%
144/1,210,018 alleles · rare
exomes 70/1,098,229 · genomes 74/111,789 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.187% | 534 |
| Admixed American | 0.0611% | 1,636 |
| Remaining individualsnot grpmax-eligible | 0.0189% | 5,291 |
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.Pro655=
- Coding
- c.1965T>G
- MANE Select
- NM_001291867
- dbSNP
- rs151009077
- Type
- single nucleotide variant
- Location
- chrX:17726071 (GRCh38)
- Structure
- AlphaFold pLDDT 43.65
- Residue 655
- the 'disordered' region
Similar variants
- NHS p.Arg248Ter Pathogenic ★★ same condition
- NHS p.Arg394Ter Pathogenic ★★ same condition
- NHS p.Arg900Ter Pathogenic ★★ same condition
- NHS p.Gln411Ter Pathogenic ★★ same condition
- NHS p.Gln80Ter Pathogenic/Likely pathogenic ★★ same condition
- NHS p.Ala564Val Uncertain significance ★★ same condition
- NHS p.Ala745Val Uncertain significance ★★ same condition
- NHS p.Arg162Cys 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-pro655 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown