NCSTN p.Pro293=
c.879A>G · rs531877039 · VCV1588157
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0426%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.019 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.9 | GERP -3.8 |
| Overall | ||
| CADD | 2.632 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0426%
African / African-American · 32/75,066 alleles
Filtering AF
0.0309%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0271%
Overall
0.00248%
40/1,614,240 alleles · ultra-rare
exomes 22/1,461,886 · genomes 18/152,354 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0426% | 2,346 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| Admixed American | 0.00167% | 60,032 |
| European (non-Finnish) | 0.000169% | 590,016 |
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
- NCSTN
- Protein
- p.Pro293=
- Coding
- c.879A>G
- MANE Select
- NM_015331
- dbSNP
- rs531877039
- Type
- single nucleotide variant
- Location
- chr1:160352089 (GRCh38)
- Gene constraint
- LOEUF 0.343 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.73 · 30 PDB
Similar variants
- NCSTN p.Ala207Pro Uncertain significance ★★ ⚠ same type
- NCSTN p.Ala298Thr Uncertain significance ★★ ⚠ same type
- NCSTN p.Ala484Thr Uncertain significance ★★ same type
- NCSTN p.Ala48Ser Uncertain significance ★★ ⚠ same type
- NCSTN p.Ala497Val Uncertain significance ★★ ⚠ same type
- NCSTN p.Ala664Gly Uncertain significance ★★ same type
- NCSTN p.Ala664Thr Uncertain significance ★★ same type
- NCSTN p.Arg105Trp 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/ncstn-p-pro293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown