TRIM63 p.Lys4=
c.12G>A · rs3795690 · VCV1298266
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 9.81%, 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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.99 | GERP -4.5, phastCons 0.002 |
| Overall | ||
| CADD | 2.413 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.81%
East Asian · 4,402/44,862 alleles
Filtering AF
9.57%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.47%
Overall
0.852%
13,751/1,614,012 alleles · common
exomes 9,392/1,461,736 · genomes 4,359/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 9.81% | 10 |
| African / African-American | 8.66% | 12 |
| Remaining individualsnot grpmax-eligible | 1.3% | 77 |
| Middle Eastern | 1.15% | 87 |
| Admixed American | 0.81% | 123 |
| South Asian | 0.282% | 354 |
| Ashkenazi Jewishnot grpmax-eligible | 0.25% | 400 |
| European (non-Finnish) | 0.0976% | 1,024 |
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
- TRIM63
- Protein
- p.Lys4=
- Coding
- c.12G>A
- MANE Select
- NM_032588
- dbSNP
- rs3795690
- Type
- single nucleotide variant
- Location
- chr1:26067483 (GRCh38)
- Gene constraint
- LOEUF 1.329 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.88 · 3 PDB
Similar variants
- TRIM63 p.Ala244Val Uncertain significance ★★ ⚠ same type
- TRIM63 p.Ala289Val Uncertain significance ★★ ⚠ same type
- TRIM63 p.Arg112Gln Uncertain significance ★★ ⚠ same type
- TRIM63 p.Arg183His Uncertain significance ★★ ⚠ same type
- TRIM63 p.Arg230Trp Uncertain significance ★★ ⚠ same type
- TRIM63 p.Arg62Gln Uncertain significance ★★ ⚠ same type
- TRIM63 p.Arg62Trp Uncertain significance ★★ ⚠ same type
- TRIM63 p.Arg74His 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/trim63-p-lys4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown