TSSC4

tumor suppressing subtransferable candidate 4

Basic information

Region (hg38): 11:2400488-2403878

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.

• not_specified (61 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. These statistics are base on transcript: NM_000005706.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			58	3	1	62
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	3	2

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