Is CAV2 p.Ser147= (c.441C>T) pathogenic?

CAV2 p.Ser147= (c.441C>T) is classified Benign in CAV2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-05-15). Common (popmax 5.19%, eas) — too common for a highly-penetrant pathogenic allele.

CAV2 p.Ser147=

Q: How common is CAV2 p.Ser147= (c.441C>T) in the general population?

CAV2 p.Ser147= (c.441C>T) is common (popmax 5.19%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.441C>T · rs117722738 · VCV779921

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 5.19%, eas) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.088	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.5	GERP -3
Overall
CADD	5.387	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 5.19% East Asian · 2,327/44,860 alleles

Filtering AF 5.01% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.94%

Overall 0.175% 2,827/1,613,866 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	5.19%	19
Remaining individualsnot grpmax-eligible	0.411%	243
South Asian	0.154%	650
African / African-American	0.0467%	2,143
Middle Eastern	0.033%	3,031
Admixed American	0.025%	4,001
European (non-Finnish)	0.00432%	23,134

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: CAV2
Protein: p.Ser147=
Coding: c.441C>T
MANE Select: NM_001233
dbSNP: rs117722738
Type: single nucleotide variant
Location: chr7:116506073 (GRCh38)
Gene constraint: LOEUF 0.938 · pLI 0.09 (gnomAD)
Structure: AlphaFold pLDDT 78.26

Full CAV2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAV2 p.Ala8Val Uncertain significance ★ ⚠ same type
CAV2 p.Arg40Gln Uncertain significance ★ ⚠ same type
CAV2 p.Asp17Ala Uncertain significance ★ ⚠ same type
CAV2 p.Asp17Tyr Uncertain significance ★ ⚠ same type
CAV2 p.Asp55Asn Uncertain significance ★ ⚠ same type
CAV2 p.Cys151Tyr Uncertain significance ★ ⚠ same type
CAV2 p.Gln158Lys Uncertain significance ★ ⚠ same type
CAV2 p.Glu26Ala 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/cav2-p-ser147 (accessed [today's date]).

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