TCP10L

t-complex 10 like

Basic information

Region (hg38): 21:32497966-32587373

Links

ENSG00000242220 ∙ NCBI:140290 ∙ OMIM:608365 ∙ HGNC:11657 ∙ Uniprot:Q8TDR4 ∙ 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 TCP10L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCP10L 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			9			9
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	1

Variants in TCP10L

This is a list of pathogenic ClinVar variants found in the TCP10L region.

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

Position	Type	Phenotype	Significance	ClinVar
21-32501436-C-T		not specified	Uncertain significance (Sep 14, 2022)
21-32503926-G-A		not specified	Uncertain significance (May 24, 2024)
21-32503934-T-G		not specified	Uncertain significance (Jul 08, 2022)
21-32504009-A-G		not specified	Uncertain significance (Jul 20, 2022)
21-32514809-T-C			Benign (Jun 01, 2018)
21-32514843-G-A		not specified	Uncertain significance (Mar 01, 2024)
21-32514918-C-A		not specified	Uncertain significance (Jan 04, 2022)
21-32514918-C-T			Likely benign (Dec 01, 2022)
21-32514921-G-A		not specified	Uncertain significance (Jul 20, 2022)
21-32515036-C-G		not specified	Uncertain significance (Jul 25, 2023)
21-32515045-G-A		not specified	Uncertain significance (Dec 14, 2021)
21-32515045-G-T			Benign (Jun 01, 2018)
21-32515079-A-T		not specified	Uncertain significance (Aug 02, 2022)
21-32515127-G-T		not specified	Uncertain significance (May 23, 2024)
21-32515173-A-G			Benign (Jul 16, 2018)
21-32576780-A-AC			Benign (Jan 22, 2018)
21-32576787-C-G		not specified	Uncertain significance (Jan 22, 2024)
21-32576842-G-A		not specified	Uncertain significance (Jan 26, 2023)
21-32578767-T-A		not specified	Uncertain significance (Jan 18, 2023)
21-32582229-G-C		not specified	Uncertain significance (Jun 10, 2024)
21-32582314-C-G		not specified	Uncertain significance (Jan 08, 2024)
21-32582333-C-T		not specified	Uncertain significance (Mar 25, 2024)
21-32582340-T-C		not specified	Uncertain significance (Mar 29, 2023)
21-32582391-G-A		not specified	Uncertain significance (Jun 30, 2022)
21-32584189-G-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCP10L	protein_coding	protein_coding	ENST00000300258	4	10822

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00330	0.841	125701	0	45	125746	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0641	122	124	0.984	0.00000681	1378
Missense in Polyphen		39	37.712	1.0342		474
Synonymous	0.384	44	47.4	0.929	0.00000287	430
Loss of Function	1.18	5	8.78	0.569	4.59e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00120	0.00120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. Has in vitro transcription inhibition activity. Acts as a tumor suppressor in hepatocellular carcinoma (HCC) cells. {ECO:0000269|PubMed:14586771, ECO:0000269|PubMed:24565846}.

Recessive Scores

• pRec: 0.0535

Intolerance Scores

• loftool: 0.749
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.0374
• hipred: N
• hipred_score: 0.112
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.111

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: transcription corepressor activity;protein binding;identical protein binding;protein self-association;repressing transcription factor binding