Is CDH7 p.Val617= (c.1851C>T) pathogenic?

CDH7 p.Val617= (c.1851C>T) is classified Benign in CDH7 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-06-09). Common (popmax 11.5%, amr) — too common for a highly-penetrant pathogenic allele.

CDH7 p.Val617=

Q: How common is CDH7 p.Val617= (c.1851C>T) in the general population?

CDH7 p.Val617= (c.1851C>T) is common (popmax 11.5%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1851C>T · rs17711596 · VCV1295063

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 11.5%, amr) — 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 -1.3	GERP -4.9
Overall
CADD	0.851	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 11.5% Admixed American · 6,911/60,008 alleles

Filtering AF 11.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 11.2%

Overall 5.21% 84,128/1,613,866 alleles · common exomes 77,769/1,461,580 · genomes 6,359/152,286 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	11.5%	9
European (non-Finnish)	5.84%	17
Remaining individualsnot grpmax-eligible	4.47%	22
Finnishnot grpmax-eligible	3.83%	26
Amishnot grpmax-eligible	2.19%	46
Ashkenazi Jewishnot grpmax-eligible	2.15%	47
South Asian	1.82%	55
Middle Eastern	0.99%	101
African / African-American	0.944%	106
East Asian	0.00668%	14,959

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.Val617=
Coding: c.1851C>T
MANE Select: NM_004361
dbSNP: rs17711596
Type: single nucleotide variant
Location: chr18:65862904 (GRCh38)
Structure: AlphaFold pLDDT 78.14

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

Similar variants

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
CDH7 c.210+52G>A Benign ★★ same type
CDH7 c.210+56T>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-val617 (accessed [today's date]).

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