Is PDZD7 p.Phe5= (c.15C>T) pathogenic?

PDZD7 p.Phe5= (c.15C>T) is classified Likely benign in PDZD7 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-27). Very rare (popmax 0.00399%, nfe).

How common is PDZD7 p.Phe5= (c.15C>T) in the general population?

PDZD7 p.Phe5= (c.15C>T) is very rare (popmax 0.00399%, nfe) (gnomAD).

PDZD7 p.Phe5=

c.15C>T · rs764821315 · VCV1968632

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00399%, 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 0.66	GERP -4.8, phastCons 0.053
Overall
CADD	7.602	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00399% European (non-Finnish) · 47/1,178,720 alleles

Filtering AF 0.00307% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00275%

Overall 0.00348% 56/1,609,318 alleles · very rare exomes 54/1,457,078 · genomes 2/152,240 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00802%	12,468
European (non-Finnish)grpmax	0.00399%	25,079
African / African-American	0.00267%	37,464
Finnishnot grpmax-eligible	0.0016%	62,328
South Asian	0.0011%	90,630

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Phe5=
Coding: c.15C>T
MANE Select: NM_001195263
dbSNP: rs764821315
Type: single nucleotide variant
Location: chr10:101030205 (GRCh38)
Gene constraint: LOEUF 1.057 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 57.10 · 2 PDB

Full PDZD7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PDZD7 p.Phe5Ile Uncertain significance ★ ⚠ same residue
PDZD7 p.Phe5fs 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-phe5 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown