BLOC1S3 p.Asp79=
c.237C>T · rs1487581109 · VCV3029583
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00794%, amr)
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 0.7 | GERP 0.37, phastCons 1 |
| Overall | ||
| CADD | 12.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00794%
Admixed American · 4/50,362 alleles
Filtering AF
0.00265%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00155%
Overall
0.000511%
7/1,370,968 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00794% | 12,590 |
| European (non-Finnish) | 0.000263% | 380,912 |
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.Asp79=
- Coding
- c.237C>T
- MANE Select
- NM_212550
- dbSNP
- rs1487581109
- Type
- single nucleotide variant
- Location
- chr19:45179533 (GRCh38)
- Gene constraint
- LOEUF 1.836 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.38
- Residue 79
- the 'disordered' region
Similar variants
- 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
- BLOC1S3 p.Gln150Arg 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-asp79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown