DSG2 p.Val149=
c.447T>C · rs1389484271 · VCV889472
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0401%, eas)
Conditions
4
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.41 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.31 | phastCons 1 |
| Overall | ||
| CADD | 3.708 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0401%
East Asian · 18/44,850 alleles
Filtering AF
0.0259%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0214%
Overall
0.00123%
18/1,461,776 alleles · ultra-rare
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
- Protein
- p.Val149=
- Coding
- c.447T>C
- MANE Select
- NM_001943
- dbSNP
- rs1389484271
- Type
- single nucleotide variant
- Location
- chr18:31521167 (GRCh38)
- Gene constraint
- LOEUF 0.764 · pLI <0.01 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.27 · 12 PDB
- Residue 149
- the cadherin 1 domain; a β-strand
Similar variants
- DSG2 p.Val149Ile Uncertain significance ★★ ⚠ same residue
- DSG2 p.Val149Phe Uncertain significance ★ ⚠ same residue
- DSG2 c.1423+1G>T Likely pathogenic ★★ same condition
- DSG2 c.1424-1G>A Likely pathogenic ★★ same condition
- DSG2 c.523+1G>T Pathogenic/Likely pathogenic ★★ same condition
- DSG2 c.690+1G>A Pathogenic ★★ same condition
- DSG2 c.81+1G>T Likely pathogenic ★★ same condition
- DSG2 c.829-2A>T Likely 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/dsg2-p-val149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown