BLOC1S3 p.Pro200=
c.600G>A · rs145239205 · VCV1336681
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0822%, 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 0.12 | GERP -3.3, phastCons 0.88 |
| Overall | ||
| CADD | 7.655 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0822%
African / African-American · 61/74,214 alleles
Filtering AF
0.0656%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0597%
Overall
0.00417%
67/1,607,948 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0822% | 1,217 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,769 |
| Admixed American | 0.00335% | 29,840 |
| East Asian | 0.00227% | 44,114 |
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
- BLOC1S3
- Protein
- p.Pro200=
- Coding
- c.600G>A
- MANE Select
- NM_212550
- dbSNP
- rs145239205
- Type
- single nucleotide variant
- Location
- chr19:45179896 (GRCh38)
- Gene constraint
- LOEUF 1.836 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.38
Similar variants
- BLOC1S3 p.Pro200Leu 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-pro200 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown