RLIM p.Phe35=
c.105T>C · VCV4951592
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.415%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.95 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.1 | GERP 0.7, phastCons 1 |
| Overall | ||
| CADD | 9.364 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.415%
European (non-Finnish) · 3,702/891,047 alleles
Filtering AF
0.404%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.4%
Overall
0.334%
4,030/1,205,166 alleles · rare
exomes 3,704/1,092,926 · genomes 326/112,240 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.415% | 241 |
| Admixed American | 0.261% | 384 |
| Remaining individualsnot grpmax-eligible | 0.249% | 402 |
| African / African-American | 0.0821% | 1,217 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0682% | 1,466 |
| Finnishnot grpmax-eligible | 0.0558% | 1,793 |
| Middle Eastern | 0.0463% | 2,158 |
| South Asian | 0.00177% | 56,452 |
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.Phe35=
- Coding
- c.105T>C
- MANE Select
- NM_016120
- Type
- single nucleotide variant
- Location
- chrX:74595873 (GRCh38)
- Structure
- AlphaFold pLDDT 50.55 · 3 PDB
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-phe35 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown