Is CEL p.Thr471= (c.1413G>A) pathogenic?

CEL p.Thr471= (c.1413G>A) is classified Uncertain significance in CEL (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-01). Very rare (popmax 0.00167%, amr).

How common is CEL p.Thr471= (c.1413G>A) in the general population?

CEL p.Thr471= (c.1413G>A) is very rare (popmax 0.00167%, amr) (gnomAD).

CEL p.Thr471=

c.1413G>A · rs779571761 · VCV2673198

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.20	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 2.9	GERP -3.5, phastCons 1
Overall
CADD	10.8	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,026 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000479% 7/1,461,864 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	60,026
Remaining individualsnot grpmax-eligible	0.0016%	62,504
African / African-American	0.00133%	75,032
South Asian	0.0011%	91,084
European (non-Finnish)	0.000254%	393,340

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.Thr471=
Coding: c.1413G>A
MANE Select: NM_001807
dbSNP: rs779571761
Type: single nucleotide variant
Location: chr9:133070587 (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

Similar variants

CEL p.Thr471Met Uncertain significance ★★ same residue
CEL p.Thr471Lys Uncertain significance ★ same residue
CEL p.Thr471Ser Uncertain significance ★ same residue
CEL p.Thr471fs Conflicting classifications of pathogenicity ★ same residue
CEL c.67-3C>A Uncertain significance ★★ same type
CEL p.Ala295Ser Uncertain significance ★★ same type
CEL p.Ala548Glu Uncertain significance ★★ same type
CEL p.Ala722Val Uncertain significance ★★ 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/cel-p-thr471 (accessed [today's date]).

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