NCAPD2 p.Asp109=
c.327T>C · VCV4915330
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.289%, 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 -1.1 | GERP -1.6, phastCons 0.003 |
| Overall | ||
| CADD | 4.924 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.289%
South Asian · 263/91,078 alleles
Filtering AF
0.26%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.249%
Overall
0.0172%
278/1,614,172 alleles · rare
exomes 263/1,461,892 · genomes 15/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.289% | 346 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,251 |
| European (non-Finnish) | 0.000424% | 236,005 |
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.Asp109=
- Coding
- c.327T>C
- MANE Select
- NM_014865
- Type
- single nucleotide variant
- Location
- chr12:6510693 (GRCh38)
- Gene constraint
- LOEUF 0.687 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.94
- Residue 109
- the 'interactions with smc2 and smc4' region
Similar variants
- NCAPD2 c.2735-6C>T Uncertain significance ★★ same type
- NCAPD2 p.Ala43Gly Uncertain significance ★★ ⚠ same type
- NCAPD2 p.Arg1397His Uncertain significance ★★ ⚠ same type
- NCAPD2 p.Arg677His Uncertain significance ★★ ⚠ same type
- NCAPD2 p.Arg952Cys Uncertain significance ★★ ⚠ same type
- NCAPD2 p.Asn509Ser Uncertain significance ★★ ⚠ same type
- NCAPD2 p.Asn598Ile Uncertain significance ★★ ⚠ same type
- NCAPD2 p.Gln670Ter 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/ncapd2-p-asp109 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown