Is ELN p.Val477del (c.1430_1432del) pathogenic?

ELN p.Val477del (c.14301432del) is classified Uncertain significance in ELN (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-21). Very rare (popmax 0.00572%, afr); Associated with supravalvular aortic stenosis.

What condition is associated with ELN p.Val477del (c.1430_1432del)?

ELN p.Val477del (c.1430_1432del) is associated with supravalvular aortic stenosis (ClinVar).

How common is ELN p.Val477del (c.1430_1432del) in the general population?

ELN p.Val477del (c.1430_1432del) is very rare (popmax 0.00572%, afr) (gnomAD).

ELN p.Val477del

c.1430_1432del · VCV3693919

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00572%, afr)

Conditions

supravalvular aortic stenosis

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -12	GERP -12
Overall
CADD	3.8	PHRED · no single calibrated threshold — expert panels disagree
Region caveats
Repeat context	tandem	(TGGTGT)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00572% African / African-American · 4/69,954 alleles

Filtering AF 0.00193% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0011%

Overall 0.000369% 5/1,354,424 alleles · very rare exomes 4/1,202,202 · genomes 1/152,222 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00572%	17,489
Ashkenazi Jewishnot grpmax-eligible	0.00357%	27,998

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: ELN
Protein: p.Val477del
Coding: c.1430_1432del
MANE Select: NM_000501
Type: Deletion
Location: chr7:74059900 (GRCh38)

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

Disease context

supravalvular aortic stenosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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/eln-p-val477del (accessed [today's date]).

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