DIXDC1 p.Asp608=
c.1824C>T · rs114428192 · VCV783647
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.56%, 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 1.4 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 10.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.56%
African / African-American · 2,670/74,928 alleles
Filtering AF
3.45%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.4%
Overall
0.215%
3,455/1,609,598 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.56% | 28 |
| Ashkenazi Jewishnot grpmax-eligible | 0.449% | 223 |
| Remaining individualsnot grpmax-eligible | 0.337% | 297 |
| Middle Eastern | 0.315% | 318 |
| Admixed American | 0.195% | 513 |
| European (non-Finnish) | 0.0248% | 4,033 |
| Finnishnot grpmax-eligible | 0.0157% | 6,389 |
| South Asian | 0.00666% | 15,021 |
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
- DIXDC1
- Protein
- p.Asp608=
- Coding
- c.1824C>T
- MANE Select
- NM_001037954
- dbSNP
- rs114428192
- Type
- single nucleotide variant
- Location
- chr11:112016758 (GRCh38)
- Gene constraint
- LOEUF 0.783 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.52 · 1 PDB
- Residue 608
- the dix domain
Similar variants
- DIXDC1 p.Asp608Glu Uncertain significance ★ ⚠ same residue
- DIXDC1 p.Asn19Asp Benign ★★ same type
- DIXDC1 p.Ala156Pro Uncertain significance ★ ⚠ same type
- DIXDC1 p.Ala25Pro Uncertain significance ★ ⚠ same type
- DIXDC1 p.Ala39Val Uncertain significance ★ ⚠ same type
- DIXDC1 p.Arg138Gln Uncertain significance ★ ⚠ same type
- DIXDC1 p.Arg199Gln Uncertain significance ★ ⚠ same type
- DIXDC1 p.Arg199Trp 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/dixdc1-p-asp608 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown