TCP10L2

t-complex 10 like 2, pseudogene

Basic information

Links

ENSG00000166984 ∙ NCBI:401285 ∙ ∙ HGNC:21254 ∙ ∙ ∙ 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 TCP10L2 gene.

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCP10L2 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				2		2
Total	0	0	0	2	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCP10L2	protein_coding	protein_coding	ENST00000366832	7	50500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.97e-8	0.312	125098	1	135	125234	0.000543

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.744	210	182	1.16	0.0000105	2186
Missense in Polyphen		49	45.247	1.0829		651
Synonymous	0.00669	76	76.1	0.999	0.00000522	671
Loss of Function	0.618	13	15.6	0.831	9.14e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00107
Ashkenazi Jewish	0.00163	0.00159
East Asian	0.000329	0.000326
Finnish	0.0000472	0.0000462
European (Non-Finnish)	0.000353	0.000335
Middle Eastern	0.000329	0.000326
South Asian	0.00148	0.00141
Other	0.000854	0.000822

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0374
• hipred: N
• hipred_score: 0.380

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00656

Gene Damage Prediction

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

Gene ontology

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