RLIM p.Pro477=
c.1431T>G · rs2079616066 · VCV2660927
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.26e-05%)
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 0.94 | phastCons 0.025 |
| Overall | ||
| CADD | 5.122 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.26e-05%
Overall
8.26e-05%
1/1,211,185 alleles · very rare
exomes 1/1,097,611 · genomes 0/113,574 · joint denominator
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
- RLIM
- Protein
- p.Pro477=
- Coding
- c.1431T>G
- MANE Select
- NM_016120
- dbSNP
- rs2079616066
- Type
- single nucleotide variant
- Location
- chrX:74591884 (GRCh38)
- Structure
- AlphaFold pLDDT 50.55 · 3 PDB
- Residue 477
- the 'disordered' region
Similar variants
- RLIM p.Pro477Leu Uncertain significance ★ ⚠ same residue
- RLIM p.Pro477_Ser480del Likely benign ★ same residue
- RLIM p.Arg365Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- RLIM p.Arg387Cys Pathogenic/Likely pathogenic ★★ same type
- RLIM p.Asp598Asn Pathogenic/Likely pathogenic ★★ same type
- RLIM p.Arg162His Uncertain significance ★★ ⚠ same type
- RLIM p.Arg372Gln Uncertain significance ★★ ⚠ same type
- RLIM p.Arg510Gln 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/rlim-p-pro477 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown