CAVIN4 p.Ser173=
c.519G>C · rs145794010 · VCV227558
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0726%, 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 -20 | GERP -5.2 |
| Overall | ||
| CADD | 0.015 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0726%
European (non-Finnish) · 857/1,179,926 alleles
Filtering AF
0.0685%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0669%
Overall
0.0555%
896/1,614,042 alleles · ultra-rare
exomes 850/1,461,784 · genomes 46/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0726% | 1,377 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,290 |
| Finnishnot grpmax-eligible | 0.00937% | 10,672 |
| African / African-American | 0.00933% | 10,717 |
| Admixed American | 0.00833% | 12,006 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,600 |
| South Asian | 0.0011% | 91,086 |
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.Ser173=
- Coding
- c.519G>C
- MANE Select
- NM_001018116
- dbSNP
- rs145794010
- Type
- single nucleotide variant
- Location
- chr9:100585875 (GRCh38)
- Gene constraint
- LOEUF 0.875 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 66.21
- Residue 173
- a modified residue (phosphoserine)
Similar variants
- CAVIN4 p.Ser173Leu Uncertain significance ★ same residue
- 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
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-ser173 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown