BLOC1S3 p.Ser33=
c.99G>C · rs2513837157 · VCV2744441
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -0.013 | GERP -3.2, phastCons 0.12 |
| Overall | ||
| CADD | 8.062 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- BLOC1S3
- Protein
- p.Ser33=
- Coding
- c.99G>C
- MANE Select
- NM_212550
- dbSNP
- rs2513837157
- Type
- single nucleotide variant
- Location
- chr19:45179395 (GRCh38)
- Gene constraint
- LOEUF 1.836 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.38
- Residue 33
- the 'disordered' region
Similar variants
- BLOC1S3 p.Ser33Leu Uncertain significance ★★ ⚠ same residue
- BLOC1S3 p.Ala103Val Uncertain significance ★★ ⚠ same type
- BLOC1S3 p.Ala169Ser Uncertain significance ★★ ⚠ same type
- BLOC1S3 p.Ala60Thr Uncertain significance ★★ ⚠ same type
- BLOC1S3 p.Arg106Pro Uncertain significance ★★ ⚠ same type
- BLOC1S3 p.Arg112Gln Uncertain significance ★★ ⚠ same type
- BLOC1S3 p.Arg112Leu Uncertain significance ★★ ⚠ same type
- BLOC1S3 p.Asp197His 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/bloc1s3-p-ser33 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown