Is ELN p.Ala258= (c.774G>A) pathogenic?

ELN p.Ala258= (c.774G>A) is classified Likely benign in ELN (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-12-29). Very rare (popmax 0.00329%, sas); Associated with supravalvular aortic stenosis.

What condition is associated with ELN p.Ala258= (c.774G>A)?

ELN p.Ala258= (c.774G>A) is associated with supravalvular aortic stenosis (ClinVar).

How common is ELN p.Ala258= (c.774G>A) in the general population?

ELN p.Ala258= (c.774G>A) is very rare (popmax 0.00329%, sas) (gnomAD).

ELN p.Ala258=

c.774G>A · rs781921056 · VCV509084

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00329%, sas)

Conditions

supravalvular aortic stenosis

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 -4	GERP -4.7
Overall
CADD	1.129	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00329% South Asian · 3/91,086 alleles

Filtering AF 0.000875% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000474%

Overall 0.00112% 18/1,613,782 alleles · very rare exomes 16/1,461,778 · genomes 2/152,004 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00329%	30,362
East Asian	0.00223%	44,896
Remaining individualsnot grpmax-eligible	0.0016%	62,478
European (non-Finnish)	0.0011%	90,764

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.Ala258=
Coding: c.774G>A
MANE Select: NM_000501
dbSNP: rs781921056
Type: single nucleotide variant
Location: chr7:74048531 (GRCh38)
Gene constraint: LOEUF 0.696 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 36.20

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

Similar variants

ELN p.Ala258Val Uncertain significance ★ ⚠ same residue
ELN c.377-2A>G Pathogenic/Likely pathogenic ★★ same condition
ELN c.643+1G>C Likely pathogenic ★★ same condition
ELN c.686-2A>G Likely pathogenic ★★ same condition
ELN c.800-1G>A Pathogenic/Likely pathogenic ★★ same condition
ELN c.800-2A>G Pathogenic ★★ same condition
ELN c.800-3C>G Pathogenic ★★ same condition
ELN c.82+1G>A Pathogenic/Likely pathogenic ★★ 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/eln-p-ala258 (accessed [today's date]).

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