RLIM p.Ser505=
c.1515A>C · rs771322184 · VCV737360
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, 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 0.048 | phastCons 0.8 |
| Overall | ||
| CADD | 6.319 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
European (non-Finnish) · 12/894,918 alleles
Filtering AF
0.000715%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000565%
Overall
0.000991%
12/1,210,944 alleles · very rare
exomes 12/1,097,474 · genomes 0/113,470 · 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.Ser505=
- Coding
- c.1515A>C
- MANE Select
- NM_016120
- dbSNP
- rs771322184
- Type
- single nucleotide variant
- Location
- chrX:74591800 (GRCh38)
- Structure
- AlphaFold pLDDT 50.55 · 3 PDB
- Residue 505
- the 'disordered' region
Similar variants
- 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
- RLIM p.Asp337Glu Uncertain significance ★★ ⚠ same type
- RLIM p.Ile246Val 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-ser505 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown