CCAR2 p.Phe847=
c.2541C>T · rs148866061 · VCV3048365
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0695%, afr)
Conditions
1
CCAR2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.054 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.37 | acceptor gain · deltas |
| Pangolin | Δ0.21 | gain · loss 0.07 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 17.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0695%
African / African-American · 52/74,820 alleles
Filtering AF
0.0544%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.049%
Overall
0.00331%
53/1,600,698 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0695% | 1,439 |
| European (non-Finnish) | 8.52e-05% | 1,174,069 |
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
- CCAR2
- Protein
- p.Phe847=
- Coding
- c.2541C>T
- MANE Select
- NM_001393997
- dbSNP
- rs148866061
- Type
- single nucleotide variant
- Location
- chr8:22619169 (GRCh38)
- Gene constraint
- LOEUF 0.288 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.61 · 1 PDB
- Residue 847
- the 'interaction with nr1d1' region
Disease context
CCAR2-related disorder
Similar variants
- CCAR2 c.150+8C>G Benign same condition
- CCAR2 c.1609-5A>G Benign same condition
- CCAR2 c.2522-3C>T Likely benign same condition
- CCAR2 p.Ala406= Benign same condition
- CCAR2 p.Ala819= Benign same condition
- CCAR2 p.Arg418Gln Likely benign same condition
- CCAR2 p.Asp292= Likely benign same condition
- CCAR2 p.Asp372= Likely benign same condition
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/ccar2-p-phe847 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown