RLIM p.Ser80=
c.240A>C · rs139400227 · VCV786708
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.44%, afr)
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 -0.9 | GERP -1.7, phastCons 0.006 |
| Overall | ||
| CADD | 8.435 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.44%
African / African-American · 1,951/56,649 alleles
Filtering AF
3.32%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.27%
Overall
0.201%
2,423/1,203,489 alleles · low-frequency
exomes 1,265/1,092,305 · genomes 1,158/111,184 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.44% | 29 |
| Remaining individualsnot grpmax-eligible | 0.312% | 320 |
| Admixed American | 0.296% | 338 |
| Middle Eastern | 0.254% | 393 |
| European (non-Finnish) | 0.0201% | 4,985 |
| Finnishnot grpmax-eligible | 0.00431% | 23,197 |
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.Ser80=
- Coding
- c.240A>C
- MANE Select
- NM_016120
- dbSNP
- rs139400227
- Type
- single nucleotide variant
- Location
- chrX:74594319 (GRCh38)
- Structure
- AlphaFold pLDDT 50.55 · 3 PDB
- Residue 80
- 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-ser80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown