Is CEL p.Thr382Met (c.1145C>T) pathogenic?

CEL p.Thr382Met (c.1145C>T) is classified Uncertain significance in CEL (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-13). Ultra-rare (popmax 0.0831%, eas); Associated with Inborn genetic diseases.

What condition is associated with CEL p.Thr382Met (c.1145C>T)?

CEL p.Thr382Met (c.1145C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CEL p.Thr382Met (c.1145C>T) in the general population?

CEL p.Thr382Met (c.1145C>T) is ultra-rare (popmax 0.0831%, eas) (gnomAD).

CEL p.Thr382Met

c.1145C>T · rs774313114 · VCV2351360

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0831%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.222	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.15	GERP 1.7
Regional constraint	o/e 0.01	constrained · MANE · 1,632 bp · p 4.1e-17 · regional, not allelic
Overall
CADD	14.39	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0831% East Asian · 35/42,126 alleles

Filtering AF 0.0613% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0538%

Overall 0.00838% 102/1,216,506 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0831%	1,204
Admixed American	0.0594%	1,685
African / African-American	0.0111%	8,989
South Asian	0.00512%	19,534
Remaining individualsnot grpmax-eligible	0.00409%	24,455
Ashkenazi Jewishnot grpmax-eligible	0.00372%	26,882
European (non-Finnish)	0.00237%	42,127

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.Thr382Met
Coding: c.1145C>T
MANE Select: NM_001807
dbSNP: rs774313114
Type: single nucleotide variant
Location: chr9:133069118 (GRCh38)
Gene constraint: LOEUF 0.972 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.10 · 7 PDB
Residue 382: an α-helix

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-thr382met (accessed [today's date]).

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