Is CDH7 p.Gly88= (c.264C>T) pathogenic?

CDH7 p.Gly88= (c.264C>T) is classified Benign in CDH7 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2018-06-27). Common (popmax 6.19%, afr) — too common for a highly-penetrant pathogenic allele.

CDH7 p.Gly88=

Q: How common is CDH7 p.Gly88= (c.264C>T) in the general population?

CDH7 p.Gly88= (c.264C>T) is common (popmax 6.19%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.264C>T · rs61741837 · VCV775401

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 6.19%, afr) — too common for a highly-penetrant pathogenic allele

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 -2.6	GERP -3
Overall
CADD	13.59	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.19% African / African-American · 4,639/74,950 alleles

Filtering AF 6.04% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.98%

Overall 0.337% 5,436/1,613,854 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	6.19%	16
Middle Eastern	0.496%	202
Admixed American	0.455%	220
Remaining individualsnot grpmax-eligible	0.44%	227
South Asian	0.0209%	4,793
European (non-Finnish)	0.0166%	6,020
Ashkenazi Jewishnot grpmax-eligible	0.00676%	14,801
East Asian	0.00223%	44,866
Finnishnot grpmax-eligible	0.00156%	64,016

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: CDH7
Protein: p.Gly88=
Coding: c.264C>T
MANE Select: NM_021153 · reported on NM_004361
dbSNP: rs61741837
Type: single nucleotide variant
Location: chr18:65809757 (GRCh38)
Structure: AlphaFold pLDDT 78.14
Residue 88: the cadherin 1 domain

Full CDH7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDH19 p.Ser88Asn Uncertain significance ★ ⚠ same residue
CDH19 p.Ser88Thr Uncertain significance ★ ⚠ same residue
CDH19 p.Pro558= Benign ★★ same type
CDH19 p.Thr89Ile Benign ★★ same type
CDH7 c.1612+22C>T Benign ★★ same type
CDH7 c.1612+24A>T Benign ★★ same type
CDH7 c.1612+81T>C Benign ★★ same type
CDH7 c.1864+225A>G Benign ★★ 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/cdh7-p-gly88 (accessed [today's date]).

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