TCP11L1

t-complex 11 like 1

Basic information

Region (hg38): 11:33039417-33105943

Links

ENSG00000176148 ∙ NCBI:55346 ∙ ∙ HGNC:25655 ∙ Uniprot:Q9NUJ3 ∙ 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 TCP11L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCP11L1 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			27			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	27	0	0

Variants in TCP11L1

This is a list of pathogenic ClinVar variants found in the TCP11L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-33043799-A-G		not specified	Uncertain significance (Dec 13, 2023)
11-33043817-A-C		not specified	Uncertain significance (Oct 07, 2022)
11-33043847-T-C		not specified	Uncertain significance (Jul 16, 2024)
11-33043891-A-G		not specified	Uncertain significance (Nov 10, 2022)
11-33043931-C-T		not specified	Uncertain significance (Apr 07, 2022)
11-33054595-A-C		not specified	Uncertain significance (Sep 20, 2024)
11-33054646-G-A		not specified	Uncertain significance (Apr 07, 2023)
11-33054655-A-G		not specified	Uncertain significance (Oct 13, 2023)
11-33054661-C-G		not specified	Uncertain significance (Apr 12, 2022)
11-33057140-G-A		not specified	Uncertain significance (Dec 07, 2023)
11-33057168-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-33057209-A-G		Exstrophy-epispadias complex	Uncertain significance (-)
11-33057209-A-T		not specified	Uncertain significance (Mar 25, 2024)
11-33057213-A-G		not specified	Uncertain significance (May 16, 2022)
11-33057221-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-33058019-C-T		not specified	Uncertain significance (Mar 31, 2022)
11-33058064-G-A		not specified	Uncertain significance (Apr 11, 2023)
11-33058123-A-G		not specified	Uncertain significance (Mar 30, 2024)
11-33058965-T-G		not specified	Uncertain significance (May 24, 2023)
11-33059064-G-T		not specified	Uncertain significance (Dec 05, 2022)
11-33061544-G-A		not specified	Uncertain significance (Aug 05, 2024)
11-33061646-A-G		not specified	Uncertain significance (Dec 08, 2023)
11-33065858-A-G		not specified	Uncertain significance (Apr 30, 2024)
11-33065897-G-A		not specified	Uncertain significance (May 16, 2023)
11-33065899-G-T		not specified	Uncertain significance (Jul 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCP11L1	protein_coding	protein_coding	ENST00000334274	9	66527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00437	0.994	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	217	275	0.788	0.0000140	3347
Missense in Polyphen		52	91.073	0.57097		1192
Synonymous	1.86	85	110	0.774	0.00000621	995
Loss of Function	2.81	8	22.3	0.359	0.00000117	266

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000109
Finnish	0.000832	0.000832
European (Non-Finnish)	0.0000971	0.0000967
Middle Eastern	0.000114	0.000109
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.758
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.1

Haploinsufficiency Scores

• pHI: 0.206
• hipred: N
• hipred_score: 0.384
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.858

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcp11l1

Gene ontology

• Cellular component: microtubule