RTCB p.Val347=
c.1041G>C · rs41310258 · VCV782754
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.05%, 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 0.15 | GERP -2.6, phastCons 0.94 |
| Overall | ||
| CADD | 5.174 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.05%
European (non-Finnish) · 12,444/1,180,008 alleles
Filtering AF
1.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.03%
Overall
0.849%
13,708/1,614,178 alleles · low-frequency
exomes 12,929/1,461,866 · genomes 779/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.05% | 95 |
| Remaining individualsnot grpmax-eligible | 0.592% | 169 |
| Ashkenazi Jewishnot grpmax-eligible | 0.372% | 269 |
| South Asian | 0.36% | 278 |
| Admixed American | 0.258% | 387 |
| Middle Eastern | 0.231% | 433 |
| Finnishnot grpmax-eligible | 0.23% | 436 |
| African / African-American | 0.155% | 647 |
| Amishnot grpmax-eligible | 0.11% | 912 |
| East Asian | 0.0512% | 1,952 |
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
- RTCB
- Protein
- p.Val347=
- Coding
- c.1041G>C
- MANE Select
- NM_014306
- dbSNP
- rs41310258
- Type
- single nucleotide variant
- Location
- chr22:32395164 (GRCh38)
- Gene constraint
- LOEUF 0.622 · pLI 0.17 (gnomAD)
- Structure
- AlphaFold pLDDT 95.66 · 5 PDB
- Residue 347
- a β-strand
Similar variants
- RTCB p.Ala276= Benign ★★ same type
- RTCB p.Ala101Thr Uncertain significance ★ ⚠ same type
- RTCB p.Ala211Val Uncertain significance ★ ⚠ same type
- RTCB p.Ala242Ser Uncertain significance ★ ⚠ same type
- RTCB p.Ala294Val Uncertain significance ★ ⚠ same type
- RTCB p.Ala296Thr Uncertain significance ★ ⚠ same type
- RTCB p.Ala333Ser Uncertain significance ★ ⚠ same type
- RTCB p.Ala333Thr 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/rtcb-p-val347 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown