KDELR3
Basic information
Region (hg38): 22:38468078-38483447
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (30 variants)
- not_provided (1 variants)
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. These statistics are base on transcript: NM_000006855.4. 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 | 0 | |||||
| missense | 28 | 28 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 28 | 0 | 0 |
GnomAD
Source:
| 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:
- 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
- Phenotype
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