NACA p.Pro959=
c.2877G>C · VCV4820963
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.328%, sas)
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 -20 | GERP -2 |
| Overall | ||
| CADD | 0.369 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.328%
South Asian · 127/38,724 alleles
Filtering AF
0.282%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.264%
Overall
0.0602%
573/951,792 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.328% | 305 |
| Admixed American | 0.225% | 445 |
| Ashkenazi Jewishnot grpmax-eligible | 0.129% | 777 |
| Middle Eastern | 0.127% | 786 |
| African / African-American | 0.115% | 869 |
| East Asian | 0.0932% | 1,073 |
| Remaining individualsnot grpmax-eligible | 0.0907% | 1,103 |
| Finnishnot grpmax-eligible | 0.0854% | 1,171 |
| European (non-Finnish) | 0.0392% | 2,554 |
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
- NACA
- Protein
- p.Pro959=
- Coding
- c.2877G>C
- MANE Select
- NM_001365896
- Type
- single nucleotide variant
- Location
- chr12:56718653 (GRCh38)
- Gene constraint
- LOEUF 0.627 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 38.15 · 26 PDB
- Residue 959
- the 'disordered' region
Similar variants
- NACA p.Ala242= Benign ★★ same type
- NACA p.Phe405Ser Benign ★★ same type
- NACA p.Pro1772Ser Benign ★★ same type
- NACA p.Pro490Arg Benign ★★ same type
- NACA p.Ala152Val Uncertain significance ★ ⚠ same type
- NACA p.Ala1803Pro Uncertain significance ★ ⚠ same type
- NACA p.Ala1833Val Uncertain significance ★ ⚠ same type
- NACA p.Ala1868Val 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/naca-p-pro959 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown