PRKCSH p.Phe384=
c.1152C>T · VCV4739952
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0114%, 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 -1.7 | GERP -2.9 |
| Overall | ||
| CADD | 7.362 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0114%
Admixed American · 6/52,662 alleles
Filtering AF
0.00488%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00338%
Overall
0.0016%
25/1,565,378 alleles · ultra-rare
exomes 25/1,413,074 · genomes 0/152,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0114% | 8,777 |
| African / African-American | 0.00406% | 24,645 |
| Remaining individualsnot grpmax-eligible | 0.0033% | 30,346 |
| South Asian | 0.00118% | 84,888 |
| European (non-Finnish) | 0.00113% | 88,816 |
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
- PRKCSH
- Protein
- p.Phe384=
- Coding
- c.1152C>T
- MANE Select
- NM_001289104
- Type
- single nucleotide variant
- Location
- chr19:11448247 (GRCh38)
- Gene constraint
- LOEUF 0.699 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 84.33 · 2 PDB
- Residue 384
- a UniProt-annotated variant site (in pcld1)
Similar variants
- PRKCSH c.683+1G>A Likely pathogenic ★★ same type
- PRKCSH c.684-1G>A Likely pathogenic ★★ same type
- PRKCSH c.762+2T>C Likely pathogenic ★★ same type
- PRKCSH p.Glu429Ter Pathogenic/Likely pathogenic ★★ same type
- PRKCSH c.1286+4C>T Uncertain significance ★★ same type
- PRKCSH p.Arg121Cys Uncertain significance ★★ ⚠ same type
- PRKCSH p.Arg121His Uncertain significance ★★ ⚠ same type
- PRKCSH p.Arg281Gln Uncertain significance ★★ ⚠ 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/prkcsh-p-phe384 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown