MDK

midkine

Basic information

Region (hg38): 11:46380756-46383837

Previous symbols: [ "NEGF2" ]

Links

ENSG00000110492NCBI:4192OMIM:162096HGNC:6972Uniprot:P21741AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MDK gene.

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
clinvar
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)3394089
11-46382314-C-G not specified Uncertain significance (Aug 12, 2021)2243574
11-46382357-C-T not specified Uncertain significance (Nov 07, 2023)3124599
11-46382431-G-T not specified Uncertain significance (Jul 25, 2023)2614142
11-46382452-G-C not specified Uncertain significance (Feb 13, 2025)3871456
11-46382587-C-T not specified Uncertain significance (May 11, 2022)2289198
11-46382617-G-T not specified Uncertain significance (Mar 25, 2024)3293842
11-46382631-G-A not specified Uncertain significance (Apr 09, 2024)3293841
11-46382661-C-G not specified Uncertain significance (Dec 17, 2024)3871455
11-46383472-A-G not specified Uncertain significance (Apr 06, 2023)2533986

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MDKprotein_codingprotein_codingENST00000405308 43070
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.2300.739125139081251470.0000320
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3317179.30.8950.00000380917
Missense in Polyphen2428.7150.8358352
Synonymous0.5572832.00.8750.00000158269
Loss of Function1.8127.250.2763.13e-785

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004760.0000462
European (Non-Finnish)0.00005530.0000532
Middle Eastern0.000.00
South Asian0.00003320.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium

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