Is CEL p.Asp697Gly (c.2090A>G) pathogenic?

CEL p.Asp697Gly (c.2090A>G) is classified Likely benign in CEL (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-10). Ultra-rare (popmax 0.0463%, sas); Associated with Inborn genetic diseases.

What condition is associated with CEL p.Asp697Gly (c.2090A>G)?

CEL p.Asp697Gly (c.2090A>G) is associated with Inborn genetic diseases (ClinVar).

How common is CEL p.Asp697Gly (c.2090A>G) in the general population?

CEL p.Asp697Gly (c.2090A>G) is ultra-rare (popmax 0.0463%, sas) (gnomAD).

CEL p.Asp697Gly

c.2090A>G · VCV4000079

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0463%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.074	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.2	GERP -0.22
Regional constraint	o/e 1.11	unconstrained · MANE · 642 bp · p 0.096 · regional, not allelic
Overall
CADD	10.89	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0463% South Asian · 37/79,892 alleles

Filtering AF 0.0345% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0304%

Overall 0.00301% 39/1,294,596 alleles · ultra-rare exomes 38/1,195,244 · genomes 1/99,352 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0463%	2,159
Remaining individualsnot grpmax-eligible	0.00195%	51,218
European (non-Finnish)	0.000104%	961,095

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: CEL
Protein: p.Asp697Gly
Coding: c.2090A>G
MANE Select: NM_001807
Type: single nucleotide variant
Location: chr9:133071592 (GRCh38)
Gene constraint: LOEUF 0.972 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.10 · 7 PDB
Residue 697: the 'disordered' region; the '17 x 11 aa tandem repeats, glycodomain, o-linked (mucin type)' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CEL p.Ala295Ser Uncertain significance ★★ same condition
CEL p.Ala548Glu Uncertain significance ★★ same condition
CEL p.Arg185Trp Uncertain significance ★★ same condition
CEL p.Arg443Trp Uncertain significance ★★ same condition
CEL p.Gln460Arg Uncertain significance ★★ same condition
CEL p.Glu710Lys Uncertain significance ★★ same condition
CEL p.Gly147Ser Uncertain significance ★★ same condition
CEL p.His68Leu 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/cel-p-asp697gly (accessed [today's date]).

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