Is EYA4 p.Pro247= (c.741A>G) pathogenic?

EYA4 p.Pro247= (c.741A>G) is classified Likely benign in EYA4 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-06-10). Very rare (popmax 0.00167%, amr); Associated with Cardiovascular phenotype.

What condition is associated with EYA4 p.Pro247= (c.741A>G)?

EYA4 p.Pro247= (c.741A>G) is associated with Cardiovascular phenotype, dilated cardiomyopathy 1J (ClinVar).

How common is EYA4 p.Pro247= (c.741A>G) in the general population?

EYA4 p.Pro247= (c.741A>G) is very rare (popmax 0.00167%, amr) (gnomAD).

EYA4 p.Pro247=

c.741A>G · rs752226573 · VCV227370

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

Cardiovascular phenotype

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 0.2	GERP -5.3, phastCons 0.16
Overall
CADD	6.579	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/59,882 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000373% 6/1,608,310 alleles · very rare exomes 1/1,456,108 · genomes 5/152,202 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,882
Remaining individualsnot grpmax-eligible	0.00161%	62,230
African / African-American	0.00134%	74,786
European (non-Finnish)	0.000255%	391,865

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: EYA4
Protein: p.Pro247=
Coding: c.741A>G
MANE Select: NM_004100
dbSNP: rs752226573
Type: single nucleotide variant
Location: chr6:133464795 (GRCh38)
Gene constraint: LOEUF 0.536 · pLI 0.86 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 63.79

Full EYA4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: dilated cardiomyopathy 1J

Similar variants

EYA4 p.Pro247Arg Uncertain significance ★★ same residue
EYA4 c.1341-2A>G Likely pathogenic ★★ same condition
EYA4 c.1739-1G>A Likely pathogenic ★★ same condition
EYA4 p.Asp194Asn Pathogenic/Likely pathogenic ★★ ⚠ same condition
EYA4 p.Trp81Ter Pathogenic/Likely pathogenic ★★ same condition
EYA4 c.1282-13A>G Uncertain significance ★★ same condition
EYA4 c.1340+3A>G Uncertain significance ★★ same condition
EYA4 c.970+5A>G Uncertain significance ★★ same condition

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/eya4-p-pro247 (accessed [today's date]).

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