NCAPD2 p.Pro1177=
c.3531C>T · rs371282922 · VCV1879224
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.199%, mid)
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 -3.7 |
| Overall | ||
| CADD | 0.587 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.199%
Middle Eastern · 11/5,534 alleles
Filtering AF
0.111%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0862%
Overall
0.00335%
54/1,613,506 alleles · rare
exomes 52/1,461,216 · genomes 2/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.199% | 503 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,803 |
| South Asian | 0.00659% | 15,172 |
| European (non-Finnish) | 0.00186% | 53,637 |
| Admixed American | 0.00167% | 60,020 |
| African / African-American | 0.00133% | 75,010 |
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.Pro1177=
- Coding
- c.3531C>T
- MANE Select
- NM_014865
- dbSNP
- rs371282922
- Type
- single nucleotide variant
- Location
- chr12:6528998 (GRCh38)
- Gene constraint
- LOEUF 0.687 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.94
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-pro1177 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown