SGCA p.Val185=
c.555C>A · rs201518390 · VCV289773
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0513%, sas)
Conditions
2
sarcoglycanopathy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.014 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.7 | GERP -2.8 |
| Overall | ||
| CADD | 2.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0513%
South Asian · 44/85,748 alleles
Filtering AF
0.0393%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.035%
Overall
0.00375%
59/1,573,584 alleles · ultra-rare
exomes 54/1,421,300 · genomes 5/152,284 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0513% | 1,949 |
| East Asian | 0.0209% | 4,776 |
| Remaining individualsnot grpmax-eligible | 0.00983% | 10,169 |
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
- SGCA
- Protein
- p.Val185=
- Coding
- c.555C>A
- MANE Select
- NM_000023
- dbSNP
- rs201518390
- Type
- single nucleotide variant
- Location
- chr17:50168543 (GRCh38)
- Gene constraint
- LOEUF 1.273 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.15
Similar variants
- SGCA c.37+6T>C Pathogenic ★★★ same condition
- SGCA c.585-1G>A Pathogenic ★★★ same condition
- SGCA c.957-11C>G Likely pathogenic ★★★ same condition
- SGCA p.Ala107Val Likely pathogenic ★★★ ⚠ same condition
- SGCA p.Arg192Ter Pathogenic ★★★ same condition
- SGCA p.Arg221Cys Likely pathogenic ★★★ same condition
- SGCA p.Arg221Pro Likely pathogenic ★★★ same condition
- SGCA p.Arg284Cys Pathogenic ★★★ ⚠ same condition
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/sgca-p-val185 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown