MTCP1

protein-coding

mature T cell proliferation 1

Gene summary

This gene was identified by involvement in some t(X;14) translocations associated with mature T-cell proliferations. This region has a complex gene structure, with a common promoter and 5' exon spliced to two different sets of 3' exons that encode two different proteins. This gene represents the upstream 13 kDa protein that is a member of the TCL1 family. This protein may be involved in leukemogenesis. [provided by RefSeq, Mar 2009]

MANE transcript

NM_001018025.4

Inheritance

—

ClinVar variants

U:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chrX:155,064,034-155,147,937

External References & Databases

Ensembl (ENSG00000214827)

Transcript & Mutation Effects

hg38 • Region Span ~83.9 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 MTCP1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001018025.4. 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						0
missense			4 clinvar			4
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	4	0	0	4

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001018025.4	RefSeq	NP_001018025.1	3	MANE Select
ENST00000369476.8	Ensembl	ENSP00000358488.3	3	MANE Select
ENST00000362018.2	Ensembl	ENSP00000355058.2	3	Standard
ENST00000362018.3	Ensembl	ENSP00000355058.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

PI3K-Akt signaling pathway - Homo sapiens (human)
Metabolism of proteins
Mitochondrial protein import

Biological Process

cell population proliferation
positive regulation of cell population proliferation
positive regulation of peptidyl-serine phosphorylation
positive regulation of protein serine/threonine kinase activity

Molecular Function

protein kinase binding
protein serine/threonine kinase activator activity

Cellular Component

protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369476
Coding exons: 3
Length: 86316
Individuals with no LoFs: 124753
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 124754
p: 0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.64	18	50.8	0.354	0.00000450	699
Missense (PolyPhen)		5	18.647	0.26814		236
Synonymous	1.43	12	20.2	0.595	0.00000196	202
Loss of Function	1.79	1	5.57	0.180	4.40e-7	70

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000074	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Enhances the phosphorylation and activation of AKT1 and AKT2. {ECO:0000269|PubMed:10983986}.;

Intolerance Scores

LoFtool: 0.420
RVIS EVS: 0.15
RVIS percentile EVS: 63.81

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.914

Gene Damage Prediction

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