NCAPD2 p.Ala342=
c.1026G>A · rs780733818 · VCV3043179
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.028%, afr)
Conditions
1
NCAPD2-related disorder
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 -3.1 | GERP -3.1 |
| Overall | ||
| CADD | 8.982 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.028%
African / African-American · 21/74,894 alleles
Filtering AF
0.0188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0157%
Overall
0.00316%
51/1,614,018 alleles · ultra-rare
exomes 36/1,461,892 · genomes 15/152,126 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.028% | 3,566 |
| Admixed American | 0.01% | 9,997 |
| South Asian | 0.00988% | 10,120 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| European (non-Finnish) | 0.00119% | 84,289 |
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
- NCAPD2
- Protein
- p.Ala342=
- Coding
- c.1026G>A
- MANE Select
- NM_014865
- dbSNP
- rs780733818
- Type
- single nucleotide variant
- Location
- chr12:6516866 (GRCh38)
- Gene constraint
- LOEUF 0.687 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.94
- Residue 342
- the 'interactions with smc2 and smc4' region
Disease context
NCAPD2-related disorder
Similar variants
- NCAPD2 p.Ala342Val Uncertain significance ★ ⚠ same residue
- NCAPD2 c.1590-10G>A Likely benign same condition
- NCAPD2 c.3654-6C>T Likely benign same condition
- NCAPD2 p.Ala1112= Likely benign same condition
- NCAPD2 p.Ala894= Likely benign same condition
- NCAPD2 p.Gly448= Likely benign same condition
- NCAPD2 p.Ile565= Benign same condition
- NCAPD2 p.Pro836Leu Benign 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/ncapd2-p-ala342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown