TCP11L2

t-complex 11 like 2

Basic information

Region (hg38): 12:106301928-106347003

Links

ENSG00000166046 ∙ NCBI:255394 ∙ OMIM:619889 ∙ HGNC:28627 ∙ Uniprot:Q8N4U5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TCP11L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCP11L2 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in TCP11L2

This is a list of pathogenic ClinVar variants found in the TCP11L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-106311161-C-T		not specified	Uncertain significance (Dec 17, 2023)
12-106314361-C-T		not specified	Uncertain significance (Oct 21, 2021)
12-106314453-G-A			Uncertain significance (Oct 02, 2019)
12-106318352-G-A		not specified	Uncertain significance (Jun 11, 2024)
12-106318355-G-A		not specified	Uncertain significance (Feb 21, 2024)
12-106318379-C-A		not specified	Uncertain significance (Mar 01, 2023)
12-106318416-C-A		not specified	Likely benign (Apr 25, 2022)
12-106318438-A-G		not specified	Uncertain significance (Feb 23, 2023)
12-106318440-C-G		not specified	Uncertain significance (Nov 05, 2021)
12-106318450-G-A		not specified	Uncertain significance (Apr 15, 2024)
12-106321492-C-G		not specified	Uncertain significance (Apr 24, 2024)
12-106321517-A-G		not specified	Uncertain significance (Jun 22, 2023)
12-106321594-A-G		not specified	Uncertain significance (May 25, 2022)
12-106321645-C-G		not specified	Uncertain significance (Jan 06, 2023)
12-106321690-A-T		not specified	Uncertain significance (Apr 01, 2024)
12-106321691-T-A		not specified	Uncertain significance (Oct 10, 2023)
12-106323514-A-G		not specified	Uncertain significance (Dec 16, 2023)
12-106323554-A-G		not specified	Uncertain significance (Oct 20, 2023)
12-106323578-C-T		not specified	Uncertain significance (Oct 20, 2021)
12-106323589-C-T		not specified	Uncertain significance (Dec 12, 2023)
12-106335654-C-G		not specified	Uncertain significance (Apr 17, 2023)
12-106335800-G-C		not specified	Uncertain significance (Dec 13, 2022)
12-106335806-C-G		not specified	Uncertain significance (Oct 27, 2021)
12-106335807-A-G		not specified	Uncertain significance (Dec 16, 2023)
12-106336039-T-C		not specified	Uncertain significance (Apr 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCP11L2	protein_coding	protein_coding	ENST00000299045	9	45087

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.47e-12	0.100	125619	0	129	125748	0.000513

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.130	282	276	1.02	0.0000137	3429
Missense in Polyphen		92	93.243	0.98667		1186
Synonymous	1.20	86	101	0.849	0.00000521	993
Loss of Function	0.589	20	23.1	0.868	0.00000122	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000587	0.000579
Ashkenazi Jewish	0.00530	0.00487
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000374	0.000369
Middle Eastern	0.000544	0.000544
South Asian	0.000430	0.000425
Other	0.000663	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.954
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.41

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.170
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.254

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcp11l2