TSSC4

tumor suppressing subtransferable candidate 4

Basic information

Region (hg38): 11:2400487-2403878

Links

ENSG00000184281 ∙ NCBI:10078 ∙ OMIM:603852 ∙ HGNC:12386 ∙ Uniprot:Q9Y5U2 ∙ 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 TSSC4 gene.

• Inborn genetic diseases (22 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSSC4 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			20	2	1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	2

Variants in TSSC4

This is a list of pathogenic ClinVar variants found in the TSSC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-2402689-C-T		not specified	Uncertain significance (Jan 18, 2022)
11-2402701-C-T		not specified	Uncertain significance (Dec 28, 2023)
11-2402712-G-A		not specified	Uncertain significance (Jul 13, 2021)
11-2402748-A-G		not specified	Uncertain significance (Mar 24, 2023)
11-2402768-A-C		not specified	Uncertain significance (Feb 03, 2022)
11-2402823-G-A		not specified	Uncertain significance (Jan 23, 2024)
11-2402827-C-T		not specified	Uncertain significance (May 24, 2023)
11-2402900-C-G		not specified	Uncertain significance (Jan 12, 2024)
11-2402950-G-A		not specified	Likely benign (Mar 29, 2022)
11-2402983-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-2403004-G-A			Benign (Mar 29, 2018)
11-2403025-G-A		not specified	Likely benign (Nov 12, 2021)
11-2403085-C-T		not specified	Uncertain significance (Mar 29, 2022)
11-2403114-C-T		not specified	Uncertain significance (May 08, 2023)
11-2403147-G-A		not specified	Uncertain significance (Apr 03, 2023)
11-2403150-G-C		not specified	Uncertain significance (Mar 29, 2023)
11-2403168-C-G		not specified	Uncertain significance (Oct 02, 2023)
11-2403202-G-T		not specified	Uncertain significance (Dec 26, 2023)
11-2403225-G-A		Inborn genetic diseases	Uncertain significance (Nov 29, 2021)
11-2403229-C-T		not specified	Uncertain significance (May 17, 2023)
11-2403246-C-T		not specified	Uncertain significance (Dec 28, 2022)
11-2403292-G-A		not specified	Uncertain significance (Feb 16, 2023)
11-2403357-G-A		not specified	Uncertain significance (Jul 05, 2022)
11-2403423-G-A		not specified	Uncertain significance (Apr 13, 2022)
11-2403445-G-C		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSSC4	protein_coding	protein_coding	ENST00000333256	1	3389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0445	0.685	124650	0	3	124653	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.646	225	199	1.13	0.0000124	2074
Missense in Polyphen		62	59.453	1.0428		651
Synonymous	-1.46	114	95.8	1.19	0.00000684	733
Loss of Function	0.562	2	3.06	0.653	1.28e-7	42

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000581	0.0000544
Finnish	0.0000552	0.0000465
European (Non-Finnish)	0.00000901	0.00000891
Middle Eastern	0.0000581	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.637
• rvis_EVS: 1.02
• rvis_percentile_EVS: 91.02

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.123
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.574

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tssc4

Gene ontology

• Molecular function: protein binding