DSG1 p.Phe54=
c.162C>T · rs778383508 · VCV1942989
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -10 | GERP -3.8 |
| Overall | ||
| CADD | 1.726 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000991%
16/1,613,796 alleles · ultra-rare
exomes 14/1,461,740 · genomes 2/152,056 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| Finnishnot grpmax-eligible | 0.00469% | 21,338 |
| South Asian | 0.00439% | 22,770 |
| African / African-American | 0.00401% | 24,952 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| European (non-Finnish) | 0.000339% | 294,975 |
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.Phe54=
- Coding
- c.162C>T
- MANE Select
- NM_001942
- dbSNP
- rs778383508
- Type
- single nucleotide variant
- Location
- chr18:31326951 (GRCh38)
- Gene constraint
- LOEUF 0.455 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 62.93
- Residue 54
- the 'required for interaction with erbin' region; a UniProt-annotated variant site (in ppks1; uncertain significance; reduces expression of krt10 in keratinocytes); the cadherin 1 domain
Similar variants
- DSG1 p.Phe54Leu Uncertain significance ★ ⚠ same residue
- 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
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-phe54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown