PDZD7 p.Pro799=
c.2397G>T · rs759844154 · VCV1536483
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0286%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.31 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -4.3 |
| Overall | ||
| CADD | 0.008 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0286%
South Asian · 24/84,042 alleles
Filtering AF
0.0197%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0167%
Overall
0.00163%
25/1,534,424 alleles · ultra-rare
exomes 25/1,382,278 · genomes 0/152,146 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0286% | 3,502 |
| European (non-Finnish) | 8.73e-05% | 1,145,638 |
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
- PDZD7
- Protein
- p.Pro799=
- Coding
- c.2397G>T
- MANE Select
- NM_001195263
- dbSNP
- rs759844154
- Type
- single nucleotide variant
- Location
- chr10:101010492 (GRCh38)
- Gene constraint
- LOEUF 1.057 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.10 · 2 PDB
- Residue 799
- a UniProt-annotated variant site (in dfnb57); the 'disordered' region
Similar variants
- PDZD7 p.Pro799Arg Uncertain significance ★★ ⚠ same residue
- PDZD7 p.Pro799Leu Uncertain significance ★ ⚠ same residue
- PDZD7 c.1749+2T>G Likely pathogenic ★★ same type
- PDZD7 c.1750-2A>G Likely pathogenic ★★ same type
- PDZD7 c.1933+1G>A Pathogenic/Likely pathogenic ★★ same type
- PDZD7 c.928+1G>A Likely pathogenic ★★ same type
- PDZD7 p.Arg309Ter Pathogenic/Likely pathogenic ★★ same type
- PDZD7 p.Arg59Ter 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/pdzd7-p-pro799 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown