TUSC1

tumor suppressor candidate 1

Basic information

Region (hg38): 9:25676969-25678444

Links

ENSG00000198680 ∙ NCBI:286319 ∙ OMIM:610529 ∙ HGNC:31010 ∙ Uniprot:Q2TAM9 ∙ 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 TUSC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUSC1 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			20	4		24
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	4	0

Variants in TUSC1

This is a list of pathogenic ClinVar variants found in the TUSC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-25677694-G-A		not specified	Likely benign (Dec 19, 2022)
9-25677708-G-A		not specified	Uncertain significance (Mar 16, 2024)
9-25677715-G-A		not specified	Uncertain significance (Jul 25, 2023)
9-25677730-A-C		not specified	Uncertain significance (Oct 04, 2022)
9-25677732-T-G		not specified	Likely benign (Sep 28, 2022)
9-25677766-C-G		not specified	Uncertain significance (Jan 16, 2024)
9-25677772-G-A		not specified	Uncertain significance (Jul 19, 2022)
9-25677847-C-T		not specified	Uncertain significance (Feb 16, 2023)
9-25677891-T-C		not specified	Likely benign (Apr 18, 2023)
9-25677933-C-A		not specified	Likely benign (Jun 06, 2022)
9-25678017-C-T		not specified	Uncertain significance (Apr 15, 2024)
9-25678056-A-G		not specified	Uncertain significance (Sep 29, 2023)
9-25678072-G-C		not specified	Uncertain significance (Jan 26, 2023)
9-25678092-C-A		not specified	Uncertain significance (Jun 11, 2024)
9-25678111-T-C		not specified	Uncertain significance (Mar 07, 2024)
9-25678114-C-T		not specified	Uncertain significance (Feb 06, 2023)
9-25678157-G-T		not specified	Uncertain significance (Jan 31, 2024)
9-25678177-C-T		not specified	Uncertain significance (Apr 18, 2023)
9-25678216-G-C		not specified	Uncertain significance (Aug 09, 2021)
9-25678242-C-T		not specified	Uncertain significance (Oct 02, 2023)
9-25678245-C-A		not specified	Uncertain significance (Aug 02, 2021)
9-25678247-G-T		not specified	Uncertain significance (Jun 22, 2023)
9-25678248-T-C		not specified	Uncertain significance (Jul 27, 2021)
9-25678252-C-G		not specified	Uncertain significance (May 26, 2024)
9-25678255-C-A		not specified	Uncertain significance (May 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUSC1	protein_coding	protein_coding	ENST00000358022	1	2461

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0427	0.677	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.514	119	104	1.14	0.00000485	1270
Missense in Polyphen		46	51.046	0.90115		614
Synonymous	0.0136	47	47.1	0.997	0.00000213	469
Loss of Function	0.527	2	2.98	0.671	1.33e-7	31

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

Recessive Scores

• pRec: 0.0771

Haploinsufficiency Scores

• pHI: 0.0659
• hipred: N
• hipred_score: 0.238
• ghis: 0.382

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.133

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tusc1