DTX4 p.Ala342=
c.1026G>A · rs61736707 · VCV716948
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.29%, 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 -9.4 | GERP -3.5 |
| Overall | ||
| CADD | 0.452 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.29%
African / African-American · 967/75,012 alleles
Filtering AF
1.22%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.19%
Overall
0.0728%
1,174/1,613,642 alleles · low-frequency
exomes 605/1,461,360 · genomes 569/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.29% | 78 |
| Middle Eastern | 0.169% | 591 |
| Admixed American | 0.115% | 870 |
| Remaining individualsnot grpmax-eligible | 0.107% | 932 |
| European (non-Finnish) | 0.00466% | 21,452 |
| East Asian | 0.00446% | 22,433 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
| South Asian | 0.0033% | 30,338 |
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
- DTX4
- Protein
- p.Ala342=
- Coding
- c.1026G>A
- MANE Select
- NM_015177
- dbSNP
- rs61736707
- Type
- single nucleotide variant
- Location
- chr11:59189190 (GRCh38)
- Gene constraint
- LOEUF 0.732 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.83
Similar variants
- DTX4 p.Thr284= Benign ★★ same type
- DTX4 p.Val257Gly Benign ★★ same type
- DTX4 p.Val355= Benign ★★ same type
- DTX4 p.Ala171Thr Uncertain significance ★ ⚠ same type
- DTX4 p.Ala288Pro Uncertain significance ★ ⚠ same type
- DTX4 p.Ala303Gly Uncertain significance ★ ⚠ same type
- DTX4 p.Ala310Thr Uncertain significance ★ ⚠ same type
- DTX4 p.Ala40Gly 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/dtx4-p-ala342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown