Is CAVIN4 p.Ser190= (c.570A>T) pathogenic?

CAVIN4 p.Ser190= (c.570A>T) is classified Benign in CAVIN4 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2016-09-23). Common (popmax 19.8%, eas) — too common for a highly-penetrant pathogenic allele.

CAVIN4 p.Ser190=

Q: How common is CAVIN4 p.Ser190= (c.570A>T) in the general population?

CAVIN4 p.Ser190= (c.570A>T) is common (popmax 19.8%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.570A>T · rs28623148 · VCV226741

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 19.8%, 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.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.9	GERP -0.71, phastCons 1
Overall
CADD	7.838	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 19.8% East Asian · 8,866/44,862 alleles

Filtering AF 19.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 19.3%

Overall 3.9% 62,940/1,614,118 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	19.8%	5
South Asian	18.4%	5
African / African-American	5.36%	19
Remaining individualsnot grpmax-eligible	4.58%	22
Admixed American	3.46%	29
Middle Eastern	3.3%	30
European (non-Finnish)	2.27%	44
Ashkenazi Jewishnot grpmax-eligible	2.15%	47
Finnishnot grpmax-eligible	1.17%	85
Amishnot grpmax-eligible	0.11%	912

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: CAVIN4
Protein: p.Ser190=
Coding: c.570A>T
MANE Select: NM_001018116
dbSNP: rs28623148
Type: single nucleotide variant
Location: chr9:100585926 (GRCh38)
Gene constraint: LOEUF 0.875 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 66.21

Full CAVIN4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAVIN4 p.Arg17Cys Uncertain significance ★★ ⚠ same type
CAVIN4 p.Arg272Cys Uncertain significance ★★ ⚠ same type
CAVIN4 p.Asn128Lys Uncertain significance ★★ ⚠ same type
CAVIN4 p.Pro142Leu Uncertain significance ★★ ⚠ same type
CAVIN4 p.Ser20Thr Uncertain significance ★★ ⚠ same type
CAVIN4 c.408+28T>C Likely benign ★★ same type
CAVIN4 c.408+42T>C Benign ★★ same type
CAVIN4 c.408+6C>A 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/cavin4-p-ser190 (accessed [today's date]).

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