CAVIN4 p.Glu313=
c.939G>A · rs778284038 · VCV227561
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0143%, nfe)
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 | GERP -1.9, phastCons 0.21 |
| Overall | ||
| CADD | 1.904 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0143%
European (non-Finnish) · 169/1,179,248 alleles
Filtering AF
0.0125%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0119%
Overall
0.0112%
181/1,612,786 alleles · ultra-rare
exomes 175/1,460,678 · genomes 6/152,108 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0143% | 6,978 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,922 |
| Admixed American | 0.00501% | 19,972 |
| African / African-American | 0.00267% | 37,438 |
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.Glu313=
- Coding
- c.939G>A
- MANE Select
- NM_001018116
- dbSNP
- rs778284038
- Type
- single nucleotide variant
- Location
- chr9:100586295 (GRCh38)
- Gene constraint
- LOEUF 0.875 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 66.21
- Residue 313
- the 'disordered' region
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-glu313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown