DSG2 c.1015del
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
3
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 0.59, phastCons 1 |
| Non-coding constraint | Z 0.70 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 35.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,914 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000434%
7/1,613,676 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 74,914 |
| European (non-Finnish) | 0.000509% | 196,655 |
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
- DSG2
- Coding
- c.1015del
- MANE Select
- NM_001943
- dbSNP
- rs794728094
- Type
- Deletion
- Location
- chr18:31530986 (GRCh38)
- Gene constraint
- LOEUF 0.764 · pLI <0.01 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.27 · 12 PDB
Similar variants
- DSG2 c.2001_2001+5del Likely pathogenic ★★ same condition
- DSG2 c.523+1_523+2del Likely pathogenic ★★ same condition
- DSG2 p.Asn462fs Pathogenic/Likely pathogenic ★★ same condition
- DSG2 p.Leu171fs Pathogenic/Likely pathogenic ★★ same condition
- DSG2 p.Phe211fs Pathogenic ★★ same condition
- DSG2 p.Thr31fs Pathogenic/Likely pathogenic ★★ same condition
- DSG2 p.Val103fs Pathogenic/Likely pathogenic ★★ same condition
- DSG2 c.1423+5del Uncertain significance ★★ 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/dsg2-c-1015del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown