RAP2C p.Thr178=
c.534A>C · rs139834013 · VCV789464
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.7%, eas)
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 6.2 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 12.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.7%
East Asian · 909/33,724 alleles
Filtering AF
2.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.49%
Overall
0.131%
1,585/1,207,758 alleles · low-frequency
exomes 1,481/1,095,552 · genomes 104/112,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.7% | 37 |
| Finnishnot grpmax-eligible | 0.41% | 244 |
| South Asian | 0.218% | 460 |
| Ashkenazi Jewishnot grpmax-eligible | 0.173% | 577 |
| Remaining individualsnot grpmax-eligible | 0.168% | 594 |
| Middle Eastern | 0.0922% | 1,084 |
| European (non-Finnish) | 0.026% | 3,851 |
| Admixed American | 0.0175% | 5,713 |
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
- RAP2C
- Protein
- p.Thr178=
- Coding
- c.534A>C
- MANE Select
- NM_001271186
- dbSNP
- rs139834013
- Type
- single nucleotide variant
- Location
- chrX:132214186 (GRCh38)
- Structure
- AlphaFold pLDDT 91.23
Similar variants
- RAP2C p.Arg2Lys Uncertain significance ★ ⚠ same type
- RAP2C p.Asp174Tyr Uncertain significance ★ ⚠ same type
- RAP2C p.Leu156Val Uncertain significance ★ ⚠ same type
- RAP2C p.Lys73Arg Uncertain significance ★ ⚠ same type
- RAP2C p.Phe28Leu Uncertain significance ★ ⚠ same type
- RAP2C p.Val81Ile Uncertain significance ★ ⚠ same type
- RAP2C p.Tyr106= Likely 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/rap2c-p-thr178 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown