PDZD7 p.Arg643=
c.1929G>A · rs560900265 · VCV1595754
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0998%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.17 | GERP -3.2, phastCons 0.38 |
| Overall | ||
| CADD | 6.506 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0998%
African / African-American · 73/73,152 alleles
Filtering AF
0.0813%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0746%
Overall
0.00581%
90/1,550,236 alleles · ultra-rare
exomes 37/1,397,908 · genomes 53/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0998% | 1,002 |
| Admixed American | 0.0235% | 4,251 |
| Remaining individualsnot grpmax-eligible | 0.00832% | 12,012 |
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.Arg643=
- Coding
- c.1929G>A
- MANE Select
- NM_001195263
- dbSNP
- rs560900265
- Type
- single nucleotide variant
- Location
- chr10:101011929 (GRCh38)
- Gene constraint
- LOEUF 1.057 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.10 · 2 PDB
- Residue 643
- a UniProt-annotated variant site (in dfnb57)
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-arg643 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown