MGP

matrix Gla protein, the group of Gla domain containing

Basic information

Region (hg38): 12:14880864-14885857

Links

ENSG00000111341NCBI:4256OMIM:154870HGNC:7060Uniprot:P08493AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Keutel syndrome (Definitive), mode of inheritance: AR
  • Keutel syndrome (Strong), mode of inheritance: AR
  • Keutel syndrome (Supportive), mode of inheritance: AR
  • Keutel syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Keutel syndromeARCardiovascularThe condition can involve congenital cardiac anomalies, and awareness may allow early managementCardiovascular; Craniofacial; Dermatologic; Musculoskeletal; Neurologic6468443; 3717211; 2515061; 9674914; 9916809; 15810001

ClinVar

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

  • not_provided (84 variants)
  • Keutel_syndrome (16 variants)
  • MGP-related_disorder (7 variants)
  • not_specified (3 variants)
  • Inborn_genetic_diseases (3 variants)
  • Spondyloepiphyseal_dysplasia (1 variants)
  • Short_palm (1 variants)
  • Short_stature (1 variants)
  • Platyspondyly (1 variants)
  • Short_distal_phalanx_of_finger (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000900.5. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
14
clinvar
15
missense
2
clinvar
29
clinvar
3
clinvar
1
clinvar
35
nonsense
1
clinvar
1
clinvar
2
start loss
0
frameshift
1
clinvar
1
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
3
Total 3 4 32 17 1

Highest pathogenic variant AF is 0.0000273042

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MGPprotein_codingprotein_codingENST00000228938 54746
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00003610.384125705041257090.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1166971.80.9620.00000442826
Missense in Polyphen3028.7621.043325
Synonymous-0.2012725.71.050.00000167227
Loss of Function0.20977.620.9184.09e-788

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001230.000123
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001760.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Associates with the organic matrix of bone and cartilage. Thought to act as an inhibitor of bone formation.;
Disease
DISEASE: Keutel syndrome (KTLS) [MIM:245150]: An autosomal recessive disorder characterized by abnormal cartilage calcification, peripheral pulmonary stenosis neural hearing loss and midfacial hypoplasia. {ECO:0000269|PubMed:9916809}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Warfarin Pathway, Pharmacodynamics;NOTCH1 regulation of human endothelial cell calcification;Endochondral Ossification;Validated transcriptional targets of AP1 family members Fra1 and Fra2 (Consensus)

Intolerance Scores

loftool
0.545
rvis_EVS
0.77
rvis_percentile_EVS
86.95

Haploinsufficiency Scores

pHI
0.157
hipred
N
hipred_score
0.182
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.539

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Mgp
Phenotype
renal/urinary system phenotype; skeleton phenotype; respiratory 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); growth/size/body region 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); muscle phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
cartilage condensation;ossification;cell differentiation;regulation of bone mineralization
Cellular component
extracellular matrix;collagen-containing extracellular matrix;extracellular exosome
Molecular function
extracellular matrix structural constituent;calcium ion binding;protein binding;structural constituent of bone