BCORL1 p.Pro1185=
c.3555G>A · rs61754128 · VCV759837
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0599%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.066 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.71 | GERP -1.6, phastCons 0.008 |
| Overall | ||
| CADD | 6.424 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0599%
South Asian · 33/55,085 alleles
Filtering AF
0.0438%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0383%
Overall
0.0364%
436/1,199,439 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0599% | 1,669 |
| European (non-Finnish) | 0.0423% | 2,364 |
| Remaining individualsnot grpmax-eligible | 0.036% | 2,776 |
| Admixed American | 0.00916% | 10,915 |
| African / African-American | 0.0089% | 11,236 |
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
- BCORL1
- Protein
- p.Pro1185=
- Coding
- c.3555G>A
- MANE Select
- NM_001379451
- dbSNP
- rs61754128
- Type
- single nucleotide variant
- Location
- chrX:130021098 (GRCh38)
- Structure
- AlphaFold pLDDT 38.79 · 2 PDB
- Residue 1185
- the 'disordered' region; a UniProt-annotated variant site (found in a sterile man with oligoasthenoteratozoospermia; likely pathogenic; loss of nuclear localization; loss of interaction with skp1)
Similar variants
- BCORL1 p.Ala261Val Uncertain significance ★★ ⚠ same type
- BCORL1 p.Arg1334Gln Uncertain significance ★★ ⚠ same type
- BCORL1 p.Arg1716Gln Uncertain significance ★★ ⚠ same type
- BCORL1 p.Asp77Val Uncertain significance ★★ ⚠ same type
- BCORL1 p.Gln1076Arg Uncertain significance ★★ ⚠ same type
- BCORL1 p.Glu1201Gln Uncertain significance ★★ ⚠ same type
- BCORL1 p.Glu1256Asp Uncertain significance ★★ ⚠ same type
- BCORL1 p.Glu1744Lys 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/bcorl1-p-pro1185 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown