HDLBP p.Asp463=
c.1389C>T · rs35168887 · VCV778058
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.91%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.083 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.6 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 12.43 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.91%
African / African-American · 2,915/74,488 alleles
Filtering AF
3.79%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.75%
Overall
0.213%
3,426/1,605,412 alleles · low-frequency
exomes 1,704/1,453,070 · genomes 1,722/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.91% | 26 |
| Middle Eastern | 0.515% | 194 |
| Admixed American | 0.314% | 318 |
| Remaining individualsnot grpmax-eligible | 0.277% | 361 |
| Ashkenazi Jewishnot grpmax-eligible | 0.117% | 856 |
| South Asian | 0.0157% | 6,389 |
| European (non-Finnish) | 0.00679% | 14,717 |
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
- HDLBP
- Protein
- p.Asp463=
- Coding
- c.1389C>T
- MANE Select
- NM_005336
- dbSNP
- rs35168887
- Type
- single nucleotide variant
- Location
- chr2:241249964 (GRCh38)
- Gene constraint
- LOEUF 0.283 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.80 · 8 PDB
- Residue 463
- the kh 5 domain; an α-helix
Similar variants
- HDLBP p.Thr630Arg Uncertain significance ★★ ⚠ same type
- HDLBP p.Gly670= Likely benign ★★ same type
- HDLBP p.Thr28Ala Benign ★★ same type
- HDLBP c.1731+1G>A Uncertain significance ★ same type
- HDLBP p.Ala232Val Uncertain significance ★ ⚠ same type
- HDLBP p.Ala238Thr Uncertain significance ★ ⚠ same type
- HDLBP p.Ala27Asp Uncertain significance ★ ⚠ same type
- HDLBP p.Ala57Val 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/hdlbp-p-asp463 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown