AGR3

anterior gradient 3, protein disulphide isomerase family member, the group of Protein disulfide isomerases

Basic information

Region (hg38): 7:16859412-16881987

Links

ENSG00000173467 ∙ NCBI:155465 ∙ OMIM:609482 ∙ HGNC:24167 ∙ Uniprot:Q8TD06 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AGR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGR3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in AGR3

This is a list of pathogenic ClinVar variants found in the AGR3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-16859598-A-G		not specified	Uncertain significance (Jan 24, 2024)
7-16860514-C-T		not specified	Likely benign (Mar 03, 2022)
7-16860530-A-T		not specified	Uncertain significance (Mar 29, 2022)
7-16860571-G-C		not specified	Uncertain significance (May 14, 2024)
7-16861393-T-C		not specified	Uncertain significance (Nov 08, 2021)
7-16861417-C-G		not specified	Uncertain significance (Jun 01, 2023)
7-16873819-A-C		not specified	Uncertain significance (Aug 17, 2021)
7-16878590-C-T		not specified	Uncertain significance (Apr 07, 2023)
7-16878596-C-T		not specified	Uncertain significance (Mar 01, 2024)
7-16878602-G-T		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGR3	protein_coding	protein_coding	ENST00000310398	7	22583

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.21e-19	0.0000368	125347	0	391	125738	0.00156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.897	106	83.0	1.28	0.00000377	1072
Missense in Polyphen		37	28.93	1.279		392
Synonymous	0.337	25	27.2	0.918	0.00000123	293
Loss of Function	-3.07	22	11.0	2.00	4.66e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00167	0.00167
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000492	0.000489
Finnish	0.000971	0.000971
European (Non-Finnish)	0.00230	0.00229
Middle Eastern	0.000492	0.000489
South Asian	0.00126	0.00124
Other	0.00278	0.00277

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for calcium-mediated regulation of ciliary beat frequency and mucociliary clearance in the airway. Might be involved in the regulation of intracellular calcium in tracheal epithelial cells. {ECO:0000250|UniProtKB:Q8R3W7}.

Recessive Scores

• pRec: 0.119

Intolerance Scores

• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.274
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.224

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Agr3

Gene ontology

• Biological process: biological_process;negative regulation of cell death
• Cellular component: cellular_component;endoplasmic reticulum;intracellular membrane-bounded organelle
• Molecular function: dystroglycan binding;protein binding