Is ECEL1 p.Arg702Gln (c.2105G>A) pathogenic?

ECEL1 p.Arg702Gln (c.2105G>A) is classified Benign/Likely benign in ECEL1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2020-08-25). AlphaMissense: likely benign (0.0776); Low-frequency (popmax 2.83%, eas).

How common is ECEL1 p.Arg702Gln (c.2105G>A) in the general population?

ECEL1 p.Arg702Gln (c.2105G>A) is low-frequency (popmax 2.83%, eas) (gnomAD).

What do computational predictors say about ECEL1 p.Arg702Gln (c.2105G>A)?

AlphaMissense predicts likely benign (score 0.0776) — an in-silico prediction, not a clinical call.

ECEL1 p.Arg702Gln

c.2105G>A · rs117012322 · VCV713063

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0776 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.83%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.0776	likely benign
REVEL	0.356	indeterminate
SaProt	LLR -6.50	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 3.7, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 6,497 bp · p 0.15 · regional, not allelic
Overall
CADD	27.1	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.83% East Asian · 1,268/44,876 alleles

Filtering AF 2.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.64%

Overall 0.14% 2,255/1,614,118 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	2.83%	35
Admixed American	1.15%	87
South Asian	0.143%	701
Remaining individualsnot grpmax-eligible	0.117%	856
Middle Eastern	0.0495%	2,021
African / African-American	0.028%	3,574
Finnishnot grpmax-eligible	0.00625%	15,997
European (non-Finnish)	0.00551%	18,154

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.Arg702Gln
Coding: c.2105G>A
MANE Select: NM_004826
dbSNP: rs117012322
Type: single nucleotide variant
Location: chr2:232480764 (GRCh38)
Gene constraint: LOEUF 1.099 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.62
Residue 702: a disulfide bond; the peptidase m13 domain

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

Similar variants

ECEL1 p.Arg702Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
ECEL1 p.Arg702Trp Uncertain significance ★ ⚠ same residue
ECEL1 c.1685+1G>A Pathogenic ★★ same type
ECEL1 c.2151+2T>C Likely pathogenic ★★ same type
ECEL1 c.966+1G>A Pathogenic ★★ same type
ECEL1 p.Ala675Thr Pathogenic ★★ same type
ECEL1 p.Arg333Ter Pathogenic ★★ same type
ECEL1 p.Arg395Gln Pathogenic/Likely pathogenic ★★ ⚠ same type

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-arg702gln (accessed [today's date]).

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