PDZD7 p.Pro336=
c.1008C>T · rs144469613 · VCV178525
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 9 submitters
gnomAD v4.1
Rare
rare (popmax 0.956%, nfe)
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 0.27 | GERP -2.5, phastCons 0.95 |
| Overall | ||
| CADD | 13.64 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.956%
European (non-Finnish) · 11,012/1,151,990 alleles
Filtering AF
0.941%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.935%
Overall
0.823%
12,719/1,545,728 alleles · rare
exomes 11,658/1,393,340 · genomes 1,061/152,388 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.956% | 105 |
| Finnishnot grpmax-eligible | 0.864% | 116 |
| Amishnot grpmax-eligible | 0.768% | 130 |
| Ashkenazi Jewishnot grpmax-eligible | 0.743% | 135 |
| Remaining individualsnot grpmax-eligible | 0.671% | 149 |
| Admixed American | 0.597% | 168 |
| Middle Eastern | 0.495% | 202 |
| South Asian | 0.267% | 375 |
| African / African-American | 0.166% | 601 |
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.Pro336=
- Coding
- c.1008C>T
- MANE Select
- NM_001195263
- dbSNP
- rs144469613
- Type
- single nucleotide variant
- Location
- chr10:101019138 (GRCh38)
- Gene constraint
- LOEUF 1.057 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.10 · 2 PDB
- Residue 336
- 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-pro336 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown