MCTP1

protein-coding

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

Gene summary

Enables calcium ion binding activity. Predicted to be involved in several processes, including modulation of chemical synaptic transmission; negative regulation of endocytosis; and negative regulation of response to oxidative stress. Located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024717.7

Inheritance

—

ClinVar variants

U:116B:7

Top phenotype

Neuromuscular disease

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr5:94,703,690-95,285,094

External References & Databases

Ensembl (ENSG00000175471)

Transcript & Mutation Effects

hg38 • Region Span ~581.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MCTP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 104

not providedTotal: 3

Neuromuscular diseaseTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024717.7. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar	3 clinvar	6
missense			105 clinvar	3 clinvar		108
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	116	4	3	123

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 71 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024717.7	RefSeq	NP_078993.4	23	MANE Select
ENST00000515393.6	Ensembl	ENSP00000424126.1	23	MANE Select
NM_001002796.5	RefSeq	NP_001002796.1	23	Standard
NM_001297777.3	RefSeq	NP_001284706.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

calcium-mediated signaling
negative regulation of cell migration
negative regulation of endocytosis
regulation of neurotransmitter secretion
regulation of neuronal synaptic plasticity

Molecular Function

calcium ion binding
calcium-dependent phospholipid binding

Cellular Component

endoplasmic reticulum membrane
integral component of membrane
cell junction
synaptic vesicle membrane
recycling endosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000515393
Coding exons: 23
Length: 580834
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125748
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.23	418	495	0.844	0.0000246	6434
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00032	0.00031	rare
Latino/Admixed American	0.00014	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00023	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.282

Gene Damage Prediction

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