DSG1 p.Phe803=
c.2409C>T · rs747276192 · VCV1109051
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0217%, 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 -6.9 | GERP -3.8 |
| Overall | ||
| CADD | 0.526 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0217%
Admixed American · 13/60,022 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0101%
Overall
0.00582%
94/1,614,136 alleles · ultra-rare
exomes 85/1,461,884 · genomes 9/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0217% | 4,617 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| East Asian | 0.00669% | 14,959 |
| European (non-Finnish) | 0.00551% | 18,154 |
| African / African-American | 0.004% | 25,009 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| South Asian | 0.00329% | 30,359 |
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
- DSG1
- Protein
- p.Phe803=
- Coding
- c.2409C>T
- MANE Select
- NM_001942
- dbSNP
- rs747276192
- Type
- single nucleotide variant
- Location
- chr18:31354605 (GRCh38)
- Gene constraint
- LOEUF 0.455 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 62.93
- Residue 803
- a UniProt-annotated variant site (in ppks1; uncertain significance; reduces expression of krt10 in keratinocytes); a UniProt-annotated variant site (in ppks1; uncertain significance; reduces protein expression, expression of krt10 and loricrin and increases phosphorylated erk in keratinocytes); a UniProt-annotated variant site (in ppks1; uncertain significance; loss of intact desmosome cell-cell junctions and retracted keratin intermediate filaments at the cell periphery of keratinocytes in the upper spinous and granular layers)
Similar variants
- DSG1 p.Arg128Ter Pathogenic ★★ same type
- DSG1 p.Arg144Ter Pathogenic ★★ same type
- DSG1 p.Arg219Ter Pathogenic ★★ same type
- DSG1 p.Arg242Ter Pathogenic ★★ same type
- DSG1 p.Arg26Ter Pathogenic ★★ same type
- DSG1 p.Arg45Ter Pathogenic/Likely pathogenic ★★ same type
- DSG1 p.Arg887Ter Pathogenic/Likely pathogenic ★★ same type
- DSG1 p.Gln81Ter Pathogenic/Likely pathogenic ★★ 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/dsg1-p-phe803 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown