KDELR3

KDEL endoplasmic reticulum protein retention receptor 3, the group of KDEL endoplasmic reticulum protein retention receptors

Basic information

Region (hg38): 22:38468078-38483447

Links

ENSG00000100196 ∙ NCBI:11015 ∙ OMIM:619900 ∙ HGNC:6306 ∙ Uniprot:O43731 ∙ 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 KDELR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDELR3 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in KDELR3

This is a list of pathogenic ClinVar variants found in the KDELR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-38468241-T-C		not specified	Uncertain significance (Dec 27, 2022)
22-38468271-T-C		not specified	Uncertain significance (Apr 09, 2024)
22-38474546-C-G		not specified	Uncertain significance (Jun 16, 2023)
22-38474558-G-C		not specified	Uncertain significance (Aug 11, 2022)
22-38474613-C-T		not specified	Uncertain significance (Dec 17, 2023)
22-38479596-G-T		not specified	Uncertain significance (Nov 28, 2023)
22-38479605-C-T		not specified	Uncertain significance (Jan 10, 2023)
22-38479627-A-G		not specified	Uncertain significance (May 26, 2022)
22-38479648-G-A		not specified	Uncertain significance (Feb 05, 2024)
22-38481230-A-T		not specified	Uncertain significance (Dec 17, 2023)
22-38481363-G-T		not specified	Uncertain significance (May 29, 2024)
22-38481404-G-A		not specified	Uncertain significance (Feb 28, 2023)
22-38481411-G-T		not specified	Uncertain significance (Oct 14, 2021)
22-38481434-T-C		not specified	Uncertain significance (Mar 15, 2024)
22-38481435-G-A		not specified	Uncertain significance (Sep 14, 2023)
22-38481492-A-G		not specified	Likely benign (Mar 19, 2024)
22-38481495-C-G		not specified	Uncertain significance (Oct 12, 2021)
22-38481522-A-C			Benign (Jan 03, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KDELR3	protein_coding	protein_coding	ENST00000409006	4	15386

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.38e-11	0.00878	125498	1	249	125748	0.000995

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.222	123	116	1.06	0.00000590	1436
Missense in Polyphen		24	29.708	0.80785		357
Synonymous	-0.743	54	47.5	1.14	0.00000221	442
Loss of Function	-1.51	13	8.31	1.56	3.58e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00483	0.00483
Ashkenazi Jewish	0.00367	0.00368
East Asian	0.000761	0.000761
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000361	0.000360
Middle Eastern	0.000761	0.000761
South Asian	0.000621	0.000588
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the retention of luminal endoplasmic reticulum proteins. Determines the specificity of the luminal ER protein retention system. Also required for normal vesicular traffic through the Golgi. This receptor recognizes K-D-E-L (By similarity). {ECO:0000250}.
• Pathway: Vibrio cholerae infection - Homo sapiens (human);XBP1(S) activates chaperone genes;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;adp-ribosylation factor;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.0991

Intolerance Scores

• loftool: 0.965
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.57

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.219
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0721

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kdelr3

Gene ontology

• Biological process: protein retention in ER lumen;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;protein transport;IRE1-mediated unfolded protein response
• Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;cis-Golgi network;integral component of membrane;transport vesicle
• Molecular function: ER retention sequence binding