NSDHL p.Pro296=
c.888C>G · VCV4953230
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00888%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.003 | GERP 0.2, phastCons 0.78 |
| Overall | ||
| CADD | 7.735 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00888%
East Asian · 3/33,790 alleles
Filtering AF
0.00235%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00125%
Overall
0.000248%
3/1,209,712 alleles · very rare
exomes 2/1,097,232 · genomes 1/112,480 · 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
- NSDHL
- Protein
- p.Pro296=
- Coding
- c.888C>G
- MANE Select
- NM_015922
- Type
- single nucleotide variant
- Location
- chrX:152868882 (GRCh38)
- Structure
- AlphaFold pLDDT 88.65 · 2 PDB
Similar variants
- NSDHL p.Pro296Arg Benign/Likely benign ★★ same residue
- NSDHL p.Ala290Val Uncertain significance ★★ ⚠ same type
- NSDHL p.Ala346Gly Uncertain significance ★★ ⚠ same type
- NSDHL p.Arg15Trp Uncertain significance ★★ ⚠ same type
- NSDHL p.Arg220Gly Uncertain significance ★★ ⚠ same type
- NSDHL p.Arg88Gln Uncertain significance ★★ ⚠ same type
- NSDHL p.Asn187Ser Uncertain significance ★★ ⚠ same type
- NSDHL p.Ile177Val 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/nsdhl-p-pro296 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown