TRIM63 p.Cys154=
c.462C>T · rs779566429 · VCV4076497
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, sas)
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 -4.1 | GERP -4.5 |
| Overall | ||
| CADD | 1.056 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
South Asian · 15/91,086 alleles
Filtering AF
0.0101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00811%
Overall
0.00254%
41/1,614,016 alleles · ultra-rare
exomes 34/1,461,816 · genomes 7/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0165% | 6,072 |
| East Asian | 0.0134% | 7,484 |
| African / African-American | 0.00801% | 12,486 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,823 |
| European (non-Finnish) | 0.000932% | 107,274 |
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.Cys154=
- Coding
- c.462C>T
- MANE Select
- NM_032588
- dbSNP
- rs779566429
- Type
- single nucleotide variant
- Location
- chr1:26061205 (GRCh38)
- Gene constraint
- LOEUF 1.329 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.88 · 3 PDB
- Residue 154
- the 'interaction with ttn' region
Similar variants
- TRIM63 p.Cys154Tyr Uncertain significance ★ ⚠ same residue
- 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
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-cys154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown