KDELR1
Basic information
Region (hg38): 19:48382574-48391551
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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.
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 | 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 KDELR1
This is a list of pathogenic ClinVar variants found in the KDELR1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-48384239-T-C | not specified | Uncertain significance (Sep 25, 2023) | ||
| 19-48384273-C-G | not specified | Uncertain significance (Mar 07, 2024) | ||
| 19-48384355-G-A | not specified | Uncertain significance (Jun 29, 2023) | ||
| 19-48384373-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
| 19-48389561-G-A | not specified | Uncertain significance (Nov 06, 2023) | ||
| 19-48389606-C-T | not specified | Likely benign (Jun 29, 2023) | ||
| 19-48389621-C-T | not specified | Uncertain significance (Nov 10, 2022) | ||
| 19-48391313-T-C | not specified | Uncertain significance (Feb 23, 2023) | ||
| 19-48391352-G-T | not specified | Uncertain significance (May 16, 2022) |
GnomAD
Source:
| 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:
- 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