TPT1

tumor protein, translationally-controlled 1, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 13:45333471-45341284

Links

ENSG00000133112 ∙ NCBI:7178 ∙ OMIM:600763 ∙ HGNC:12022 ∙ Uniprot:P13693 ∙ 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 TPT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPT1 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					1	1
missense			3		1	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	2

Variants in TPT1

This is a list of pathogenic ClinVar variants found in the TPT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-45337499-A-G		Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 10	risk factor (Jul 01, 2021)
13-45337514-A-C		Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 10	risk factor (Jul 01, 2021)
13-45337535-G-C		Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 10	risk factor (Jul 01, 2021)
13-45337574-A-G		Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 10	risk factor (Jul 01, 2021)
13-45338684-C-T			Benign (Jun 08, 2018)
13-45339532-T-C		not specified	Benign (Dec 12, 2023)
13-45339541-C-A		not specified	Uncertain significance (Oct 13, 2023)
13-45339547-C-T		not specified	Uncertain significance (Oct 25, 2022)
13-45340165-C-A		not specified	Uncertain significance (Oct 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPT1	protein_coding	protein_coding	ENST00000530705	5	4498

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.805	0.194	125578	0	2	125580	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	53	94.8	0.559	0.00000433	1163
Missense in Polyphen		2	10.073	0.19855		169
Synonymous	-1.33	41	31.5	1.30	0.00000143	289
Loss of Function	2.60	1	9.77	0.102	4.93e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000339	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in calcium binding and microtubule stabilization.
• Pathway: PLK1 signaling events (Consensus)

Recessive Scores

• pRec: 0.350

Intolerance Scores

• loftool: 0.749
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.676
• hipred: Y
• hipred_score: 0.783
• ghis: 0.607

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tpt1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; embryo phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: calcium ion transport;cellular calcium ion homeostasis;response to virus;regulation of apoptotic process;negative regulation of apoptotic process;negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
• Cellular component: spindle pole;extracellular space;nucleus;cytoplasm;multivesicular body;cytosol;cytoplasmic microtubule;extracellular exosome
• Molecular function: RNA binding;calcium ion binding;protein binding