Is CEL p.Thr471Ser (c.1411A>T) pathogenic?

CEL p.Thr471Ser (c.1411A>T) is classified Uncertain significance in CEL (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-05). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CEL p.Thr471Ser (c.1411A>T)?

CEL p.Thr471Ser (c.1411A>T) is associated with Inborn genetic diseases (ClinVar).

How common is CEL p.Thr471Ser (c.1411A>T) in the general population?

CEL p.Thr471Ser (c.1411A>T) is absent from gnomAD v4.1 (gnomAD).

CEL p.Thr471Ser

c.1411A>T · VCV3489962

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.065	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2	GERP -3.1
Regional constraint	o/e 0.75	unconstrained · MANE · 651 bp · p 0.0028 · regional, not allelic
Overall
CADD	2.389	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CEL
Protein: p.Thr471Ser
Coding: c.1411A>T
MANE Select: NM_001807
Type: single nucleotide variant
Location: chr9:133070585 (GRCh38)
Gene constraint: LOEUF 0.972 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.10 · 7 PDB
Residue 471: 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.Thr471Met Uncertain significance ★★ same residue
CEL p.Thr471= Uncertain significance ★ same residue
CEL p.Thr471Lys Uncertain significance ★ same residue
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

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-thr471ser (accessed [today's date]).

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