TCP10L3

t-complex 10 like 3, pseudogene

Basic information

Region (hg38): 6:167358107-167382954

Previous symbols: [ "TCP10" ]

Links

ENSG00000203690 ∙ NCBI:6953 ∙ OMIM:187020 ∙ HGNC:11656 ∙ ∙ ∙ 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 TCP10L3 gene.

• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCP10L3 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				3	2	5
Total	0	0	0	3	2

Variants in TCP10L3

This is a list of pathogenic ClinVar variants found in the TCP10L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-167373198-C-T			not provided (-)
6-167373273-G-A			not provided (-)
6-167376565-C-T			Benign (Dec 31, 2019)
6-167376622-C-T			Benign (Mar 05, 2018)
6-167376666-T-C			Likely benign (Oct 01, 2023)
6-167376672-C-T			Likely benign (Mar 29, 2018)
6-167382850-G-A			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCP10L3	protein_coding	protein_coding	ENST00000397829	7	27478

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000501	0.667	111023	0	9	111032	0.0000405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.134	165	170	0.971	0.0000104	2019
Missense in Polyphen		36	38.784	0.92821		558
Synonymous	-0.555	71	65.3	1.09	0.00000407	628
Loss of Function	1.01	10	14.1	0.709	7.48e-7	178

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	0.000366	0.000362
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.747
• rvis_EVS: 2.71
• rvis_percentile_EVS: 98.93

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0539

Gene Damage Prediction

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

Gene ontology

• Cellular component: nucleus;cytosol
• Molecular function: transcription corepressor activity