MTCP1

mature T cell proliferation 1

Basic information

Region (hg38): X:155064034-155147937

Links

ENSG00000214827 ∙ NCBI:4515 ∙ OMIM:300116 ∙ HGNC:7423 ∙ Uniprot:P56278 ∙ 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 MTCP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTCP1 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						0
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in MTCP1

This is a list of pathogenic ClinVar variants found in the MTCP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-155065650-G-C		not specified	Uncertain significance (Dec 13, 2023)
X-155065917-C-T		not specified	Uncertain significance (Dec 04, 2024)
X-155071541-TGGTGCAGGC-T			Likely benign (Jan 01, 2023)
X-155071734-T-C		Hereditary cancer-predisposing syndrome	Likely benign (Dec 01, 2015)
X-155073411-A-G			Uncertain significance (Nov 01, 2022)
X-155075674-T-C		Hereditary cancer-predisposing syndrome	Likely benign (Dec 01, 2015)
X-155078908-A-G		Hereditary cancer-predisposing syndrome	Likely benign (-)
X-155078944-A-G		Hereditary cancer-predisposing syndrome	Likely benign (Dec 01, 2015)
X-155081868-C-A		Hereditary cancer-predisposing syndrome	Likely benign (Dec 01, 2015)
X-155081874-G-A		Hereditary cancer-predisposing syndrome	Likely benign (Dec 01, 2015)
X-155089273-A-G			Likely benign (Oct 01, 2024)
X-155090380-C-T		Hereditary cancer-predisposing syndrome	Likely benign (Dec 01, 2015)
X-155098992-A-G		Hereditary cancer-predisposing syndrome	Likely benign (Dec 01, 2015)
X-155116069-C-G		not specified	Uncertain significance (Jan 03, 2024)
X-155116113-T-C		not specified	Uncertain significance (Apr 23, 2024)
X-155116702-A-G			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTCP1	protein_coding	protein_coding	ENST00000369476	3	86316

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.452	0.523	124753	0	1	124754	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	18	50.8	0.354	0.00000450	699
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000738	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000738	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhances the phosphorylation and activation of AKT1 and AKT2. {ECO:0000269|PubMed:10983986}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Metabolism of proteins;Mitochondrial protein import (Consensus)

Intolerance Scores

• loftool: 0.420
• rvis_EVS: 0.15
• rvis_percentile_EVS: 63.81

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.375
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtcp1

Gene ontology

• 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
• Cellular component: protein-containing complex
• Molecular function: protein kinase binding;protein serine/threonine kinase activator activity