DAZL p.Pro135=
c.405T>C · rs115317726 · VCV3039325
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.48%, afr)
Conditions
1
DAZL-related disorder
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 · A>C here scores Δ0.25 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -3.1 |
| Overall | ||
| CADD | 4.919 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.48%
African / African-American · 1,108/75,040 alleles
Filtering AF
1.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.38%
Overall
0.0788%
1,272/1,613,820 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.48% | 68 |
| Remaining individualsnot grpmax-eligible | 0.118% | 845 |
| Admixed American | 0.105% | 953 |
| Middle Eastern | 0.0495% | 2,019 |
| European (non-Finnish) | 0.00203% | 49,155 |
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
- DAZL
- Protein
- p.Pro135=
- Coding
- c.405T>C
- MANE Select
- NM_001351
- dbSNP
- rs115317726
- Type
- single nucleotide variant
- Location
- chr3:16596843 (GRCh38)
- Gene constraint
- LOEUF 0.2 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 57.38
Disease context
DAZL-related disorder
Similar variants
- DAZL p.Val66Glu Likely pathogenic same condition
- DAZL p.Thr54Ala Uncertain significance ⚠ same condition
- DAZL c.3+717G>A Benign same condition
- DAZL c.736-9G>A Benign same condition
- DAZL p.Glu55Asp Benign same condition
- DAZL p.Leu184= Likely benign same condition
- DAZL p.Ser65Thr Benign same condition
- DAZL p.Thr12Ala Benign same condition
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/dazl-p-pro135 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown