DIXDC1 p.Ser346=
c.1038T>C · rs182278039 · VCV729282
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.28%, eas)
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 1.1 | GERP 0.95, phastCons 1 |
| Overall | ||
| CADD | 10.89 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.28%
East Asian · 122/43,508 alleles
Filtering AF
0.24%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.225%
Overall
0.00938%
148/1,577,460 alleles · rare
exomes 115/1,425,524 · genomes 33/151,936 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.28% | 357 |
| Remaining individualsnot grpmax-eligible | 0.0393% | 2,546 |
| European (non-Finnish) | 0.000172% | 580,255 |
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.Ser346=
- Coding
- c.1038T>C
- MANE Select
- NM_001037954
- dbSNP
- rs182278039
- Type
- single nucleotide variant
- Location
- chr11:111986900 (GRCh38)
- Gene constraint
- LOEUF 0.783 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.52 · 1 PDB
Similar variants
- DIXDC1 p.Asn19Asp Benign ★★ same type
- DIXDC1 p.Asp608= 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-ser346 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown