BYSL p.Pro415=
c.1245C>G · rs149587548 · VCV2656545
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.329%, 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 -20 | GERP -4.4 |
| Overall | ||
| CADD | 0.017 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.329%
European (non-Finnish) · 3,886/1,180,034 alleles
Filtering AF
0.321%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.317%
Overall
0.274%
4,430/1,614,166 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.329% | 304 |
| Remaining individualsnot grpmax-eligible | 0.29% | 345 |
| South Asian | 0.226% | 442 |
| Ashkenazi Jewishnot grpmax-eligible | 0.169% | 592 |
| Admixed American | 0.0983% | 1,017 |
| African / African-American | 0.052% | 1,924 |
| Middle Eastern | 0.0165% | 6,062 |
| Finnishnot grpmax-eligible | 0.0109% | 9,146 |
| East Asian | 0.00223% | 44,882 |
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
- BYSL
- Protein
- p.Pro415=
- Coding
- c.1245C>G
- MANE Select
- NM_004053
- dbSNP
- rs149587548
- Type
- single nucleotide variant
- Location
- chr6:41932637 (GRCh38)
- Gene constraint
- LOEUF 0.632 · pLI 0.07 (gnomAD)
- Structure
- AlphaFold pLDDT 78.24 · 13 PDB
- Residue 415
- an α-helix
Similar variants
- MED20 p.Arg26Trp Uncertain significance ★★ ⚠ same type
- MED20 p.Met30Val Uncertain significance ★★ ⚠ same type
- BYSL p.Ala279Pro Uncertain significance ★ ⚠ same type
- BYSL p.Ala28Glu Uncertain significance ★ ⚠ same type
- BYSL p.Ala71Gly Uncertain significance ★ ⚠ same type
- BYSL p.Arg131His Uncertain significance ★ ⚠ same type
- BYSL p.Arg145His Uncertain significance ★ ⚠ same type
- BYSL p.Arg189Gln 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/bysl-p-pro415 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown