Is CAVIN4 p.Asp160= (c.480T>C) pathogenic?

CAVIN4 p.Asp160= (c.480T>C) is classified Likely benign in CAVIN4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-12-01). Very rare (popmax 0.00822%, nfe); Associated with CAVIN4-related disorder.

What condition is associated with CAVIN4 p.Asp160= (c.480T>C)?

CAVIN4 p.Asp160= (c.480T>C) is associated with CAVIN4-related disorder (ClinVar).

How common is CAVIN4 p.Asp160= (c.480T>C) in the general population?

CAVIN4 p.Asp160= (c.480T>C) is very rare (popmax 0.00822%, nfe) (gnomAD).

CAVIN4 p.Asp160=

c.480T>C · rs200636428 · VCV3029997

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00822%, nfe)

Conditions

CAVIN4-related disorder

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 -9.3	GERP -5.2
Overall
CADD	0.057	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00822% European (non-Finnish) · 97/1,179,896 alleles

Filtering AF 0.00689% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00633%

Overall 0.00663% 107/1,613,880 alleles · very rare exomes 101/1,461,738 · genomes 6/152,142 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0112%	8,926
European (non-Finnish)grpmax	0.00822%	12,164
African / African-American	0.004%	24,971

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Asp160=
Coding: c.480T>C
MANE Select: NM_001018116
dbSNP: rs200636428
Type: single nucleotide variant
Location: chr9:100585836 (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

Disease context

CAVIN4-related disorder

Similar variants

CAVIN4 p.Pro337Ala Uncertain significance ⚠ same condition
CAVIN4 p.Val132Met Uncertain significance ⚠ same condition
CAVIN4 p.Ala322fs Uncertain significance same condition
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

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-asp160 (accessed [today's date]).

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