Is ECEL1 p.Ser628= (c.1884A>G) pathogenic?

ECEL1 p.Ser628= (c.1884A>G) is classified Likely benign in ECEL1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-10-14). Very rare (popmax 0.00267%, afr); Associated with ECEL1-related disorder.

What condition is associated with ECEL1 p.Ser628= (c.1884A>G)?

ECEL1 p.Ser628= (c.1884A>G) is associated with ECEL1-related disorder (ClinVar).

How common is ECEL1 p.Ser628= (c.1884A>G) in the general population?

ECEL1 p.Ser628= (c.1884A>G) is very rare (popmax 0.00267%, afr) (gnomAD).

ECEL1 p.Ser628=

c.1884A>G · rs760203132 · VCV3061704

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00267%, 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 -20	GERP -12
Overall
CADD	0.013	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,932 alleles

Filtering AF 0.000443% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.00062% 10/1,613,636 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,466
European (non-Finnish)	0.000678%	147,501

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.Ser628=
Coding: c.1884A>G
MANE Select: NM_004826
dbSNP: rs760203132
Type: single nucleotide variant
Location: chr2:232481611 (GRCh38)
Gene constraint: LOEUF 1.099 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.62
Residue 628: 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.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
ECEL1 c.2228+4T>A Likely benign 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-ser628 (accessed [today's date]).

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