DCTN4 p.Pro431=
c.1293C>A · rs145961735 · VCV776079
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.99%, afr)
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 0.46 | GERP -1.1, phastCons 0.99 |
| Overall | ||
| CADD | 5.842 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.99%
African / African-American · 1,492/75,002 alleles
Filtering AF
1.91%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.87%
Overall
0.107%
1,729/1,613,130 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.99% | 50 |
| Admixed American | 0.0966% | 1,035 |
| Middle Eastern | 0.096% | 1,042 |
| Remaining individualsnot grpmax-eligible | 0.0849% | 1,178 |
| European (non-Finnish) | 0.0101% | 9,916 |
| South Asian | 0.0022% | 45,508 |
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
- DCTN4
- Protein
- p.Pro431=
- Coding
- c.1293C>A
- MANE Select
- NM_016221
- dbSNP
- rs145961735
- Type
- single nucleotide variant
- Location
- chr5:150711239 (GRCh38)
- Gene constraint
- LOEUF 0.549 · pLI 0.87 (gnomAD)
- Structure
- AlphaFold pLDDT 84.78 · 2 PDB
Similar variants
- DCTN4 p.Pro431Leu Uncertain significance ★ ⚠ same residue
- DCTN4 p.Ala195Thr Uncertain significance ★ ⚠ same type
- DCTN4 p.Ala221Thr Uncertain significance ★ ⚠ same type
- DCTN4 p.Ala22Val Uncertain significance ★ ⚠ same type
- DCTN4 p.Ala2Ser Uncertain significance ★ ⚠ same type
- DCTN4 p.Arg143Trp Uncertain significance ★ ⚠ same type
- DCTN4 p.Arg162Gln Uncertain significance ★ ⚠ same type
- DCTN4 p.Arg169Gln 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/dctn4-p-pro431 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown