MCTP1

multiple C2 and transmembrane domain containing 1, the group of Multiple C2 and transmembrane domain containing

Basic information

Region (hg38): 5:94703689-95285094

Links

ENSG00000175471 ∙ NCBI:79772 ∙ OMIM:616296 ∙ HGNC:26183 ∙ Uniprot:Q6DN14 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MCTP1 gene.

• Inborn genetic diseases (24 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCTP1 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					3	3
missense			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	3

Variants in MCTP1

This is a list of pathogenic ClinVar variants found in the MCTP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-94707532-A-C		not specified	Uncertain significance (Feb 28, 2024)
5-94707558-G-C		not specified	Uncertain significance (Dec 15, 2023)
5-94708567-A-G		not specified	Uncertain significance (Aug 22, 2023)
5-94710819-C-G		not specified	Uncertain significance (Jan 08, 2024)
5-94710851-A-G		not specified	Uncertain significance (May 08, 2023)
5-94779158-C-T			Benign (May 09, 2018)
5-94799021-G-A		not specified	Uncertain significance (Nov 08, 2022)
5-94870446-T-C		not specified	Uncertain significance (Dec 28, 2023)
5-94870946-C-T		not specified	Uncertain significance (May 18, 2022)
5-94871335-C-T		not specified	Uncertain significance (Sep 20, 2023)
5-94871365-G-C		not specified	Uncertain significance (Jun 06, 2023)
5-94888886-G-A			Benign (May 09, 2018)
5-94888915-T-C		not specified	Uncertain significance (Apr 05, 2023)
5-94894698-A-T		not specified	Uncertain significance (Jun 26, 2023)
5-94894707-T-C		not specified	Uncertain significance (Oct 10, 2023)
5-94894721-T-C			Benign (Jun 04, 2018)
5-94909332-T-C		not specified	Uncertain significance (Sep 12, 2023)
5-94912834-C-T		not specified	Uncertain significance (Jun 22, 2023)
5-94942427-C-T		not specified	Uncertain significance (Feb 16, 2023)
5-94953302-T-C		not specified	Uncertain significance (Jan 29, 2024)
5-94953307-C-T		not specified	Uncertain significance (Dec 20, 2023)
5-95017378-C-T		not specified	Uncertain significance (Nov 23, 2021)
5-95017439-C-T		not specified	Uncertain significance (Apr 28, 2022)
5-95017462-G-T		not specified	Uncertain significance (Nov 22, 2023)
5-95283867-C-G		not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MCTP1	protein_coding	protein_coding	ENST00000515393	23	580834

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000931	1.00	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	418	495	0.844	0.0000246	6434
Missense in Polyphen		113	192.55	0.58686		2552
Synonymous	-1.04	215	196	1.09	0.0000102	1946
Loss of Function	4.47	17	51.7	0.329	0.00000260	629

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000452	0.000445
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.000163	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.000233	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium sensor which is essential for the stabilization of normal baseline neurotransmitter release and for the induction and long-term maintenance of presynaptic homeostatic plasticity. {ECO:0000250|UniProtKB:A1ZBD6}.

Recessive Scores

• pRec: 0.0890

Intolerance Scores

• loftool: 0.711
• rvis_EVS: -1.51
• rvis_percentile_EVS: 3.54

Haploinsufficiency Scores

• pHI: 0.656
• hipred: Y
• hipred_score: 0.585
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.282

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Mctp1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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

Gene ontology

• Biological process: calcium-mediated signaling;negative regulation of cell migration;negative regulation of endocytosis;regulation of neurotransmitter secretion;regulation of neuronal synaptic plasticity;negative regulation of response to oxidative stress
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;cell junction;synaptic vesicle membrane;recycling endosome
• Molecular function: calcium ion binding;calcium-dependent phospholipid binding