TUSC2

tumor suppressor 2, mitochondrial calcium regulator

Basic information

Region (hg38): 3:50320027-50328251

Previous symbols: [ "PDAP2" ]

Links

ENSG00000114383 ∙ NCBI:11334 ∙ OMIM:607052 ∙ HGNC:17034 ∙ Uniprot:O75896 ∙ 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 TUSC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUSC2 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in TUSC2

This is a list of pathogenic ClinVar variants found in the TUSC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-50320047-T-C		HYAL2 deficiency	Pathogenic (Dec 14, 2021)
3-50320067-C-G		Inborn genetic diseases	Uncertain significance (May 04, 2022)
3-50320137-T-C		Inborn genetic diseases	Uncertain significance (Feb 03, 2022)
3-50320140-A-G		HYAL2-related disorder	Uncertain significance (Mar 09, 2023)
3-50320174-G-A			Uncertain significance (Dec 01, 2023)
3-50320296-G-C		HYAL2 deficiency	Pathogenic (Dec 14, 2021)
3-50320300-C-T		HYAL2 deficiency	Likely pathogenic (Apr 14, 2021)
3-50320322-G-T		Inborn genetic diseases	Uncertain significance (Mar 01, 2023)
3-50320375-C-T		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
3-50320438-A-C			Benign (Jun 09, 2021)
3-50320483-C-G		Inborn genetic diseases	Uncertain significance (May 16, 2022)
3-50320498-C-T			Likely benign (Feb 24, 2021)
3-50326153-C-T		not specified	Uncertain significance (May 31, 2022)
3-50326161-C-T		not specified	Uncertain significance (Jan 08, 2024)
3-50328075-G-A		not specified	Uncertain significance (Dec 14, 2022)
3-50328083-G-A		not specified	Uncertain significance (Aug 10, 2021)
3-50328084-A-G		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUSC2	protein_coding	protein_coding	ENST00000232496	3	8225

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.767	0.225	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	35	57.9	0.605	0.00000323	683
Missense in Polyphen		3	11.994	0.25013		151
Synonymous	1.30	15	22.9	0.654	0.00000135	226
Loss of Function	2.04	0	4.82	0.00	2.92e-7	53

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a tumor suppressor, inhibiting colony formation, causing G1 arrest and ultimately inducing apoptosis in homozygous 3p21.3 120-kb region-deficient cells.
• Pathway: miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.0942

Haploinsufficiency Scores

• pHI: 0.277
• hipred: N
• hipred_score: 0.429
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tusc2
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); neoplasm; immune system phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: natural killer cell differentiation;phagocytosis;inflammatory response;cell cycle;cell-cell signaling;cell population proliferation;interleukin-15 production;negative regulation of interleukin-17 production;positive regulation of interleukin-10 production;cell maturation;regulation of mitochondrial membrane potential;response to defense-related host reactive oxygen species production;neutrophil mediated killing of gram-negative bacterium;chemokine (C-C motif) ligand 5 production;regulation of reactive oxygen species metabolic process
• Cellular component: mitochondrion
• Molecular function: protein binding