MDK
Basic information
Region (hg38): 11:46380756-46383837
Previous symbols: [ "NEGF2" ]
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 MDK 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 | |||||
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 | 0 | 0 |
Variants in MDK
This is a list of pathogenic ClinVar variants found in the MDK region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
11-46382082-C-T | not specified | Uncertain significance (Oct 01, 2024) | ||
11-46382314-C-G | not specified | Uncertain significance (Aug 12, 2021) | ||
11-46382357-C-T | not specified | Uncertain significance (Nov 07, 2023) | ||
11-46382431-G-T | not specified | Uncertain significance (Jul 25, 2023) | ||
11-46382452-G-C | not specified | Uncertain significance (Feb 13, 2025) | ||
11-46382587-C-T | not specified | Uncertain significance (May 11, 2022) | ||
11-46382617-G-T | not specified | Uncertain significance (Mar 25, 2024) | ||
11-46382631-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
11-46382661-C-G | not specified | Uncertain significance (Dec 17, 2024) | ||
11-46383472-A-G | not specified | Uncertain significance (Apr 06, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MDK | protein_coding | protein_coding | ENST00000405308 | 4 | 3070 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.230 | 0.739 | 125139 | 0 | 8 | 125147 | 0.0000320 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.331 | 71 | 79.3 | 0.895 | 0.00000380 | 917 |
Missense in Polyphen | 24 | 28.715 | 0.8358 | 352 | ||
Synonymous | 0.557 | 28 | 32.0 | 0.875 | 0.00000158 | 269 |
Loss of Function | 1.81 | 2 | 7.25 | 0.276 | 3.13e-7 | 85 |
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 | 0.0000476 | 0.0000462 |
European (Non-Finnish) | 0.0000553 | 0.0000532 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000332 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Developmentally regulated, secreted growth factor homologous to pleiotrophin (PTN), which has heparin binding activity. Binds anaplastic lymphoma kinase (ALK) which induces ALK activation and subsequent phosphorylation of the insulin receptor substrate (IRS1), followed by the activation of mitogen-activated protein kinase (MAPK) and PI3-kinase, and the induction of cell proliferation. Involved in neointima formation after arterial injury, possibly by mediating leukocyte recruitment. Also involved in early fetal adrenal gland development (By similarity). {ECO:0000250, ECO:0000269|PubMed:12122009, ECO:0000269|PubMed:1768439}.;
- Pathway
- NOTCH-Core;Signal Transduction;Signaling by NOTCH2;Signaling by NOTCH;NOTCH2 Activation and Transmission of Signal to the Nucleus;Glypican 2 network;Beta1 integrin cell surface interactions;Alpha4 beta1 integrin signaling events;Syndecan-4-mediated signaling events
(Consensus)
Intolerance Scores
- loftool
- 0.312
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58
Haploinsufficiency Scores
- pHI
- 0.390
- hipred
- Y
- hipred_score
- 0.767
- ghis
- 0.577
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.972
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Low | Low |
Primary Immunodeficiency | Medium | Low | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mdk
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; immune system phenotype; skeleton phenotype; renal/urinary system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- mdka
- Affected structure
- retina
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- behavioral fear response;signal transduction;Notch signaling pathway;nervous system development;short-term memory;response to wounding;regulation of signaling receptor activity;cell migration;dentate gyrus development;cerebellar granular layer development;cerebral cortex development;cell differentiation;adrenal gland development;defecation;response to drug;negative regulation of neuron apoptotic process;positive regulation of transcription, DNA-templated;regulation of behavior;response to glucocorticoid;positive regulation of cell division
- Cellular component
- extracellular region;cytoplasm;cell projection;collagen-containing extracellular matrix
- Molecular function
- growth factor activity;heparin binding