RABL6 p.Pro557=
c.1671C>T · rs201053581 · VCV720671
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.351%, 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 -8.5 | GERP -1.9 |
| Overall | ||
| CADD | 0.815 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.351%
European (non-Finnish) · 4,143/1,179,682 alleles
Filtering AF
0.342%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.339%
Overall
0.277%
4,471/1,612,404 alleles · rare
exomes 4,190/1,460,090 · genomes 281/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.351% | 285 |
| Remaining individualsnot grpmax-eligible | 0.234% | 428 |
| Admixed American | 0.0901% | 1,110 |
| Finnishnot grpmax-eligible | 0.089% | 1,123 |
| African / African-American | 0.06% | 1,668 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0338% | 2,960 |
| South Asian | 0.0176% | 5,686 |
| East Asian | 0.00223% | 44,860 |
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
- RABL6
- Protein
- p.Pro557=
- Coding
- c.1671C>T
- MANE Select
- NM_024718
- dbSNP
- rs201053581
- Type
- single nucleotide variant
- Location
- chr9:136839399 (GRCh38)
- Gene constraint
- LOEUF 0.588 · pLI 0.15 (gnomAD)
- Structure
- AlphaFold pLDDT 60.84
- Residue 557
- the 'disordered' region
Similar variants
- RABL6 p.Pro557Leu Uncertain significance ★ ⚠ same residue
- RABL6 p.Arg690Gln Uncertain significance ★★ ⚠ same type
- RABL6 p.Ser402Thr Uncertain significance ★★ ⚠ same type
- RABL6 p.Ser535Gly Uncertain significance ★★ ⚠ same type
- RABL6 p.Arg280His Benign/Likely benign ★★ same type
- RABL6 p.Arg533His Benign ★★ same type
- RABL6 p.Pro518Leu Benign ★★ same type
- RABL6 p.Pro539= 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/rabl6-p-pro557 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown