KDELR1

KDEL endoplasmic reticulum protein retention receptor 1, the group of KDEL endoplasmic reticulum protein retention receptors

Basic information

Region (hg38): 19:48382575-48391551

Links

ENSG00000105438

∙ NCBI:10945 ∙ OMIM:131235 ∙ HGNC:6304 ∙ Uniprot:P24390 ∙ 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 KDELR1 gene.

not_specified (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDELR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006801.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			14 clinvar	1 clinvar		15
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	18	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KDELR1	protein_coding	protein_coding	ENST00000330720	5	8984

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.881	0.119	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.32	52	125	0.416	0.00000712	1364
Missense in Polyphen		18	52.806	0.34087		568
Synonymous	-0.674	65	58.4	1.11	0.00000395	416
Loss of Function	2.84	1	11.3	0.0883	5.39e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Required for the retention of luminal endoplasmic reticulum resident proteins via vesicular recycling. This receptor recognizes the C-terminal K-D-E-L motif. COPI-coated transport intermediates, either in the form of round vesicles or as tubular processes, mediate retrograde traffic of the KDEL receptor-ligand complexes. Also required for normal vesicular traffic through the Golgi. {ECO:0000269|PubMed:11703931}.;
Pathway: Vibrio cholerae infection - Homo sapiens (human);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;Arf1 pathway;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: 0.151

Intolerance Scores

loftool: 0.323
rvis_EVS: -0.1
rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

pHI: 0.119
hipred: Y
hipred_score: 0.598
ghis: 0.636

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.799

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Kdelr1
Phenotype: hematopoietic system phenotype; immune system phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process: T cell cytokine production;protein retention in ER lumen;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;T cell differentiation;T cell apoptotic process
Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cis-Golgi network;membrane;integral component of membrane;transport vesicle;COPI-coated vesicle membrane;endoplasmic reticulum-Golgi intermediate compartment membrane
Molecular function: KDEL sequence binding