Is CDH10 p.Arg472= (c.1416C>T) pathogenic?

CDH10 p.Arg472= (c.1416C>T) is classified Likely benign in CDH10 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-01). Very rare (popmax 0.00317%, nfe).

How common is CDH10 p.Arg472= (c.1416C>T) in the general population?

CDH10 p.Arg472= (c.1416C>T) is very rare (popmax 0.00317%, nfe) (gnomAD).

CDH10 p.Arg472=

c.1416C>T · rs139927244 · VCV2655376

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00317%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -7.5	GERP -3.7
Overall
CADD	0.303	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00317% European (non-Finnish) · 37/1,166,246 alleles

Filtering AF 0.00234% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00204%

Overall 0.0118% 189/1,598,588 alleles · very rare exomes 174/1,446,458 · genomes 15/152,130 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.44%	227
Remaining individualsnot grpmax-eligible	0.0307%	3,259
European (non-Finnish)grpmax	0.00317%	31,520
Admixed American	0.00167%	59,912
African / African-American	0.00134%	74,512
South Asian	0.0011%	90,730

Ashkenazi Jewish 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: CDH10
Protein: p.Arg472=
Coding: c.1416C>T
MANE Select: NM_006727
dbSNP: rs139927244
Type: single nucleotide variant
Location: chr5:24498497 (GRCh38)
Gene constraint: LOEUF 0.655 · pLI 0.18 (gnomAD)
Structure: AlphaFold pLDDT 78.29
Residue 472: the cadherin 4 domain

Full CDH10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDH10 p.Met316Ile Uncertain significance ★★ ⚠ same type
CDH10 p.Thr159Met Uncertain significance ★★ ⚠ same type
CDH10 p.Glu469= Benign ★★ same type
CDH10 p.Gly673= Benign ★★ same type
CDH10 p.Ala296Thr Uncertain significance ★ ⚠ same type
CDH10 p.Ala501Val Uncertain significance ★ ⚠ same type
CDH10 p.Ala530Val Uncertain significance ★ ⚠ same type
CDH10 p.Arg128Cys Uncertain significance ★ ⚠ 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/cdh10-p-arg472 (accessed [today's date]).

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