Is HDLBP p.Asp190= (c.570T>C) pathogenic?

HDLBP p.Asp190= (c.570T>C) is classified Likely benign in HDLBP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-01). Ultra-rare (popmax 0.0164%, mid); Associated with HDLBP-related disorder.

What condition is associated with HDLBP p.Asp190= (c.570T>C)?

HDLBP p.Asp190= (c.570T>C) is associated with HDLBP-related disorder (ClinVar).

How common is HDLBP p.Asp190= (c.570T>C) in the general population?

HDLBP p.Asp190= (c.570T>C) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

HDLBP p.Asp190=

c.570T>C · rs776255083 · VCV3042691

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Conditions

HDLBP-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.022	moderately benign-leaning
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.71	GERP -4.1
Overall
CADD	6.066	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,084 alleles

Filtering AF 0.00723% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0055%

Overall 0.000805% 13/1,614,096 alleles · ultra-rare exomes 5/1,461,890 · genomes 8/152,206 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,084
African / African-American	0.0133%	7,493
Remaining individualsnot grpmax-eligible	0.0032%	31,245

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.Asp190=
Coding: c.570T>C
MANE Select: NM_005336
dbSNP: rs776255083
Type: single nucleotide variant
Location: chr2:241256687 (GRCh38)
Gene constraint: LOEUF 0.283 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 74.80 · 8 PDB
Residue 190: the kh 1 domain

Full HDLBP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

HDLBP-related disorder

Similar variants

HDLBP p.Pro261Leu Uncertain significance ★ ⚠ same condition
HDLBP c.1081-10A>G Benign same condition
HDLBP c.-16A>T Likely benign same condition
HDLBP c.-27G>A Likely benign same condition
HDLBP p.Ala5= Likely benign same condition
HDLBP p.Asn418Ser Benign same condition
HDLBP p.Ile702= Likely benign same condition
HDLBP p.Ser262= Likely 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/hdlbp-p-asp190 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown