DAB1 p.Ser53=
c.159C>T · VCV4083986
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, 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 -3.8 | GERP -5.5 |
| Overall | ||
| CADD | 7.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,866 alleles
Filtering AF
0.00157%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00134%
Overall
0.00223%
36/1,613,904 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,433 |
| Admixed American | 0.00333% | 29,997 |
| African / African-American | 0.00267% | 37,450 |
| European (non-Finnish) | 0.00229% | 43,703 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
| Finnishnot grpmax-eligible | 0.00156% | 64,010 |
| South Asian | 0.0011% | 91,088 |
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
- DAB1
- Protein
- p.Ser53=
- Coding
- c.159C>T
- MANE Select
- NM_001365792
- Type
- single nucleotide variant
- Location
- chr1:57145338 (GRCh38)
- Gene constraint
- LOEUF 0.407 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 59.20
- Residue 53
- the pid domain
Similar variants
- DAB1 p.Ala103Val Uncertain significance ★★ ⚠ same type
- DAB1 p.Ala75Thr Uncertain significance ★★ same type
- DAB1 p.Arg41Gln Uncertain significance ★★ same type
- DAB1 p.Pro334Leu Uncertain significance ★★ ⚠ same type
- DAB1 p.Pro376Ala Uncertain significance ★★ ⚠ same type
- DAB1 p.Pro391Ser Uncertain significance ★★ ⚠ same type
- DAB1 p.Pro516Leu Uncertain significance ★★ ⚠ same type
- DAB1 p.Val240Leu 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/dab1-p-ser53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown