NCAPD3 p.Phe1035=
c.3105C>T · rs765047707 · VCV2642552
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0493%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.23 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.6 | GERP -4.7 |
| Overall | ||
| CADD | 0.445 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0493%
Middle Eastern · 3/6,080 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00716%
Overall
0.00143%
23/1,613,006 alleles · ultra-rare
exomes 20/1,460,854 · genomes 3/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0493% | 2,027 |
| Admixed American | 0.00501% | 19,975 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,216 |
| African / African-American | 0.00134% | 74,886 |
| European (non-Finnish) | 0.00119% | 84,252 |
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
- NCAPD3
- Protein
- p.Phe1035=
- Coding
- c.3105C>T
- MANE Select
- NM_015261
- dbSNP
- rs765047707
- Type
- single nucleotide variant
- Location
- chr11:134169051 (GRCh38)
- Gene constraint
- LOEUF 0.643 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.29 · 1 PDB
Similar variants
- NCAPD3 c.4388+1G>A Likely pathogenic ★★ same type
- NCAPD3 p.Ala334Thr Uncertain significance ★★ ⚠ same type
- NCAPD3 p.Arg519Cys Uncertain significance ★★ ⚠ same type
- NCAPD3 p.Gly1451Arg Uncertain significance ★★ ⚠ same type
- NCAPD3 p.Lys221Asn Uncertain significance ★★ ⚠ same type
- NCAPD3 c.1090-33A>G Benign ★★ same type
- NCAPD3 c.1215+28G>A Benign ★★ same type
- NCAPD3 c.1525+18T>A Benign ★★ 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/ncapd3-p-phe1035 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown