Is ELN p.Pro560fs (c.1679del) pathogenic?

ELN p.Pro560fs (c.1679del) is classified Pathogenic in ELN (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-20). No gnomAD frequency available for this variant; Associated with supravalvular aortic stenosis.

What condition is associated with ELN p.Pro560fs (c.1679del)?

ELN p.Pro560fs (c.1679del) is associated with supravalvular aortic stenosis (ClinVar).

How common is ELN p.Pro560fs (c.1679del) in the general population?

ELN p.Pro560fs (c.1679del) is no gnomAD frequency available for this variant (gnomAD).

ELN p.Pro560fs

c.1679del · rs2132320442 · VCV1074749

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 2.8	GERP 3, phastCons 0.89
Region caveats
Repeat context	tandem	TTGGTGCTGGCGTCCCTGGACTTGGAG simple repeat · ambiguous alignment · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ELN
Protein: p.Pro560fs
Coding: c.1679del
MANE Select: NM_000501
dbSNP: rs2132320442
Type: Deletion
Location: chr7:74060431 (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-pro560fs (accessed [today's date]).

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