DAB2 p.His89=
c.267C>T · rs147809840 · VCV750470
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.276%, 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 5.1 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 8.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.276%
African / African-American · 207/75,038 alleles
Filtering AF
0.245%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.233%
Overall
0.0145%
234/1,614,082 alleles · rare
exomes 120/1,461,802 · genomes 114/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.276% | 363 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,250 |
| Admixed American | 0.00833% | 12,000 |
| European (non-Finnish) | 0.00102% | 98,330 |
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
- DAB2
- Protein
- p.His89=
- Coding
- c.267C>T
- MANE Select
- NM_001343
- dbSNP
- rs147809840
- Type
- single nucleotide variant
- Location
- chr5:39392428 (GRCh38)
- Gene constraint
- LOEUF 0.479 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 54.33 · 3 PDB
- Residue 89
- the pid domain
Similar variants
- DAB2 p.Leu206Pro Uncertain significance ★★ ⚠ same type
- DAB2 c.571-9T>A Benign ★★ same type
- DAB2 p.Arg296= Benign ★★ same type
- DAB2 p.Arg296Cys Benign ★★ same type
- DAB2 p.Asn226= Benign ★★ same type
- DAB2 p.Gln523His Likely benign ★★ same type
- DAB2 p.Pro529= Likely benign ★★ same type
- DAB2 p.Ser227= Benign ★★ 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/dab2-p-his89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown