MCTP2

multiple C2 and transmembrane domain containing 2, the group of Multiple C2 and transmembrane domain containing

Basic information

Region (hg38): 15:94231538-94483952

Links

ENSG00000140563NCBI:55784OMIM:616297HGNC:25636Uniprot:Q6DN12AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • congenital heart defects, multiple types (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MCTP2 gene.

  • Inborn_genetic_diseases (151 variants)
  • not_provided (49 variants)
  • MCTP2-related_disorder (36 variants)
  • not_specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCTP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001385001.1. 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
21
clinvar
8
clinvar
29
missense
150
clinvar
13
clinvar
5
clinvar
168
nonsense
3
clinvar
1
clinvar
4
start loss
0
frameshift
1
clinvar
1
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
2
Total 0 0 155 37 13
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MCTP2protein_codingprotein_codingENST00000357742 22248866
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
6.03e-522.98e-1112487118761257480.00349
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.425724841.180.00002705777
Missense in Polyphen157124.311.2631524
Synonymous-0.4981921831.050.00001031631
Loss of Function-2.236850.81.340.00000289591

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.004070.00407
Ashkenazi Jewish0.0001050.0000992
East Asian0.01380.0136
Finnish0.007250.00714
European (Non-Finnish)0.001830.00177
Middle Eastern0.01380.0136
South Asian0.005130.00508
Other0.002740.00261

dbNSFP

Source: dbNSFP

Function
FUNCTION: Might play a role in the development of cardiac outflow tract. {ECO:0000269|PubMed:23773997}.;
Disease
DISEASE: Note=Heterozygosity for a 2.2-Mb deletion at chromosome 15q26.2, encompassing MCTP2, has been identified in a 10-year-old girl and her 3-year-old half brother, who had both coarctation of the aorta associated with dysmorphic features and ventricular septal defects. An intragenic MCTP2 duplication, leading to premature truncation (F697X) within the first transmembrane region of the protein, has also been observed in a male patient with a non-syndromic complex cardiac malformation involving coarctation, hypoplastic left heart, mitral atresia, bicuspid aortic valve and muscular ventricular septal defect. Although the link between left ventricular outflow tract malformations and MCTP2 could not be established, it has been proposed that defects in the MCTP2 gene may contribute to phenotype. This hypothesis is supported by the observation that Xenopus laevis embryos treated with MCTP2 morpholinos show no evidence of endocardial cushion formation at any level of the developing outflow tract (PubMed:23773997). {ECO:0000269|PubMed:23773997}.;

Recessive Scores

pRec
0.0958

Intolerance Scores

loftool
0.999
rvis_EVS
-0.19
rvis_percentile_EVS
39.31

Haploinsufficiency Scores

pHI
0.113
hipred
N
hipred_score
0.197
ghis
0.527

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.116

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Mctp2
Phenotype

Gene ontology

Biological process
multicellular organism development;calcium-mediated signaling;regulation of neurotransmitter secretion
Cellular component
nucleoplasm;cytosol;membrane;integral component of membrane;synaptic vesicle membrane
Molecular function
calcium ion binding;calcium-dependent phospholipid binding