PDZD7 p.Pro856=
c.2568C>A · rs1308552992 · VCV743769
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00411%, afr)
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 | GERP -4.6 |
| Overall | ||
| CADD | 0.083 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00411%
African / African-American · 3/73,042 alleles
Filtering AF
0.00109%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000502%
Overall
0.000326%
5/1,535,982 alleles · very rare
exomes 2/1,383,784 · genomes 3/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00411% | 24,347 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 60,036 |
| European (non-Finnish) | 8.72e-05% | 1,146,750 |
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.Pro856=
- Coding
- c.2568C>A
- MANE Select
- NM_001195263
- dbSNP
- rs1308552992
- Type
- single nucleotide variant
- Location
- chr10:101010321 (GRCh38)
- Gene constraint
- LOEUF 1.057 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.10 · 2 PDB
- Residue 856
- a UniProt-annotated variant site (in dfnb57); the 'disordered' region
Similar variants
- 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
- PDZD7 p.Cys331Ter Pathogenic/Likely pathogenic ★★ same type
- PDZD7 p.Gln515Ter 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-pro856 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown