Is CAV1 p.Val52= (c.156C>T) pathogenic?

CAV1 p.Val52= (c.156C>T) is classified Benign/Likely benign in CAV1 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-02-03). Common (popmax 11.7%, afr) — too common for a highly-penetrant pathogenic allele; Associated with pulmonary hypertension, primary, 3.

What condition is associated with CAV1 p.Val52= (c.156C>T)?

CAV1 p.Val52= (c.156C>T) is associated with pulmonary hypertension, primary, 3 (ClinVar).

CAV1 p.Val52=

Q: How common is CAV1 p.Val52= (c.156C>T) in the general population?

CAV1 p.Val52= (c.156C>T) is common (popmax 11.7%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.156C>T · rs10029 · VCV128610

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 11.7%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

pulmonary hypertension, primary, 3

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 0.45	GERP 0.98, phastCons 0.99
Overall
CADD	12.49	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 11.7% African / African-American · 8,779/75,034 alleles

Filtering AF 11.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 11.4%

Overall 0.634% 10,232/1,614,128 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	11.7%	9
Admixed American	1.03%	97
Remaining individualsnot grpmax-eligible	0.824%	121
Middle Eastern	0.561%	178
South Asian	0.0329%	3,036
European (non-Finnish)	0.0211%	4,739
Finnishnot grpmax-eligible	0.0125%	8,001

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: CAV1
Protein: p.Val52=
Coding: c.156C>T
MANE Select: NM_001753
dbSNP: rs10029
Type: single nucleotide variant
Location: chr7:116526650 (GRCh38)
Gene constraint: LOEUF 0.967 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.60 · 1 PDB
Residue 52: the 'required for homooligomerization' region

Full CAV1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

pulmonary hypertension, primary, 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CAV1 c.30+3A>G Uncertain significance ★★ same condition
CAV1 p.Arg101His Uncertain significance ★★ ⚠ same condition
CAV1 p.Arg171His Uncertain significance ★★ ⚠ same condition
CAV1 p.Gly83Ser Uncertain significance ★★ ⚠ same condition
CAV1 p.His79Arg Uncertain significance ★★ ⚠ same condition
CAV1 p.Lys86Arg Uncertain significance ★★ ⚠ same condition
CAV1 p.Phe68Val Uncertain significance ★★ ⚠ same condition
CAV1 p.Pro132Ala Uncertain significance ★★ ⚠ 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/cav1-p-val52 (accessed [today's date]).

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