Is ECEL1 p.Ala493= (c.1479C>T) pathogenic?

ECEL1 p.Ala493= (c.1479C>T) is classified Likely benign in ECEL1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-01-10). Rare (popmax 0.344%, afr); Associated with ECEL1-related disorder.

What condition is associated with ECEL1 p.Ala493= (c.1479C>T)?

ECEL1 p.Ala493= (c.1479C>T) is associated with ECEL1-related disorder (ClinVar).

How common is ECEL1 p.Ala493= (c.1479C>T) in the general population?

ECEL1 p.Ala493= (c.1479C>T) is rare (popmax 0.344%, afr) (gnomAD).

ECEL1 p.Ala493=

c.1479C>T · rs146818286 · VCV3051594

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.344%, afr)

Conditions

ECEL1-related disorder

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 -2.5	GERP -3.2
Overall
CADD	3.227	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.344% African / African-American · 258/74,974 alleles

Filtering AF 0.31% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.296%

Overall 0.0182% 293/1,611,772 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.344%	291
Middle Eastern	0.033%	3,026
Remaining individualsnot grpmax-eligible	0.0128%	7,803
Admixed American	0.0067%	14,924
South Asian	0.0022%	45,401
European (non-Finnish)	0.00161%	62,076

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: ECEL1
Protein: p.Ala493=
Coding: c.1479C>T
MANE Select: NM_004826
dbSNP: rs146818286
Type: single nucleotide variant
Location: chr2:232483443 (GRCh38)
Gene constraint: LOEUF 1.099 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.62
Residue 493: a disulfide bond; the peptidase m13 domain

Full ECEL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ECEL1-related disorder

Similar variants

ECEL1 p.Ala493Thr Uncertain significance ★ ⚠ same residue
ECEL1 p.Gln435Ter Pathogenic/Likely pathogenic ★★ same condition
ECEL1 p.Thr615Pro Likely pathogenic ★ same condition
ECEL1 p.Tyr618Ter Likely pathogenic ★ same condition
ECEL1 p.Val385= Likely pathogenic ★ same condition
ECEL1 p.Arg404Cys Conflicting classifications of pathogenicity ★ ⚠ same condition
ECEL1 p.Leu733Pro Uncertain significance ★ ⚠ same condition
ECEL1 p.Arg663Trp 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/ecel1-p-ala493 (accessed [today's date]).

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