Is ELN p.Ala590Thr (c.1768G>A) pathogenic?

ELN p.Ala590Thr (c.1768G>A) is classified Uncertain significance in ELN (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-01-28). AlphaMissense: likely benign (0.2493); Very rare (popmax 0.005%, amr); Associated with supravalvular aortic stenosis.

What condition is associated with ELN p.Ala590Thr (c.1768G>A)?

ELN p.Ala590Thr (c.1768G>A) is associated with supravalvular aortic stenosis (ClinVar).

How common is ELN p.Ala590Thr (c.1768G>A) in the general population?

ELN p.Ala590Thr (c.1768G>A) is very rare (popmax 0.005%, amr) (gnomAD).

What do computational predictors say about ELN p.Ala590Thr (c.1768G>A)?

AlphaMissense predicts likely benign (score 0.2493) — an in-silico prediction, not a clinical call.

ELN p.Ala590Thr

c.1768G>A · rs868932429 · VCV1050457

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2493 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

supravalvular aortic stenosis

Computational evidence

Protein change
AlphaMissense	0.2493	likely benign
REVEL	0.074	moderately benign-leaning
SaProt	LLR -11.71	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.6	GERP 4.2, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 41 kb · p 0.005 · regional, not allelic
Overall
CADD	22.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM A652T vs ClinVar A590T) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/60,020 alleles

Filtering AF 0.00145% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00123%

Overall 0.00239% 35/1,461,756 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.005%	20,007
East Asian	0.00446%	22,445
Remaining individualsnot grpmax-eligible	0.0032%	31,255
European (non-Finnish)	0.00212%	47,201
Finnishnot grpmax-eligible	0.00156%	63,906
African / African-American	0.00133%	75,054
South Asian	0.0011%	91,084

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.Ala590Thr
Coding: c.1768G>A
MANE Select: NM_000501
dbSNP: rs868932429
Type: single nucleotide variant
Location: chr7:74061121 (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 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
ELN c.889+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-ala590thr (accessed [today's date]).

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