PDZD7 p.Arg102=
c.306C>T · rs141305163 · VCV46210
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
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 -9.3 | GERP -5 |
| Overall | ||
| CADD | 0.348 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,896 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.00285%
46/1,614,116 alleles · ultra-rare
exomes 39/1,461,890 · genomes 7/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,483 |
| Admixed American | 0.005% | 20,003 |
| European (non-Finnish) | 0.00288% | 34,707 |
| African / African-American | 0.00267% | 37,472 |
| South Asian | 0.0011% | 91,090 |
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.Arg102=
- Coding
- c.306C>T
- MANE Select
- NM_001195263
- dbSNP
- rs141305163
- Type
- single nucleotide variant
- Location
- chr10:101023989 (GRCh38)
- Gene constraint
- LOEUF 1.057 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.10 · 2 PDB
- Residue 102
- the pdz 1 domain; a β-strand
Similar variants
- PDZD7 p.Arg102His Uncertain significance ★★ ⚠ same residue
- PDZD7 p.Arg102fs Pathogenic ★ 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-arg102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown