TCP11

t-complex 11

Basic information

Region (hg38): 6:35118070-35148610

Previous symbols: [ "D6S230E" ]

Links

ENSG00000124678 ∙ NCBI:6954 ∙ OMIM:186982 ∙ HGNC:11658 ∙ Uniprot:Q8WWU5 ∙ 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 TCP11 gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCP11 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in TCP11

This is a list of pathogenic ClinVar variants found in the TCP11 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-35118499-G-C		not specified	Uncertain significance (Nov 15, 2021)
6-35119290-G-A		not specified	Uncertain significance (Dec 28, 2023)
6-35119291-C-T		not specified	Uncertain significance (Jan 11, 2023)
6-35120241-C-T		not specified	Uncertain significance (Jun 22, 2023)
6-35120508-G-A		not specified	Uncertain significance (Jun 06, 2023)
6-35120646-C-T		not specified	Uncertain significance (Jun 03, 2022)
6-35120953-T-G		not specified	Uncertain significance (Mar 07, 2023)
6-35121034-T-G		not specified	Uncertain significance (Sep 16, 2021)
6-35121043-C-T		not specified	Uncertain significance (Jul 07, 2022)
6-35122199-T-C		not specified	Uncertain significance (Feb 12, 2024)
6-35122201-T-C		not specified	Uncertain significance (Sep 07, 2022)
6-35122238-C-A		not specified	Uncertain significance (Feb 01, 2023)
6-35122256-G-C		not specified	Uncertain significance (Sep 01, 2021)
6-35122288-A-G		not specified	Uncertain significance (Oct 25, 2023)
6-35122295-T-C		not specified	Uncertain significance (Apr 14, 2022)
6-35129156-A-G		not specified	Uncertain significance (Sep 22, 2023)
6-35129174-C-T		not specified	Uncertain significance (Jun 21, 2023)
6-35136198-T-A		not specified	Uncertain significance (Oct 26, 2022)
6-35140753-G-T		not specified	Uncertain significance (May 18, 2023)
6-35140756-G-T		not specified	Uncertain significance (Oct 06, 2022)
6-35140789-G-A		not specified	Uncertain significance (Jun 06, 2023)
6-35140818-C-T		not specified	Uncertain significance (Nov 17, 2022)
6-35141225-G-C		not specified	Likely benign (Nov 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCP11	protein_coding	protein_coding	ENST00000311875	10	30540

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-7	0.787	125627	0	120	125747	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.872	231	271	0.851	0.0000139	3360
Missense in Polyphen		47	81.222	0.57866		1150
Synonymous	1.16	91	106	0.857	0.00000544	1015
Loss of Function	1.41	14	21.0	0.667	9.52e-7	273

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000554	0.000554
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.00131	0.00131
Finnish	0.0000946	0.0000924
European (Non-Finnish)	0.000658	0.000633
Middle Eastern	0.00131	0.00131
South Asian	0.0000654	0.0000327
Other	0.000357	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the process of sperm capacitation and acrosome reactions. Probable receptor for the putative fertilization-promoting peptide (FPP) at the sperm membrane that may modulate the activity of the adenylyl cyclase cAMP pathway. {ECO:0000250|UniProtKB:Q01755}.

Recessive Scores

• pRec: 0.0873

Intolerance Scores

• loftool: 0.933
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.55

Haploinsufficiency Scores

• pHI: 0.0988
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.749

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcp11
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;protein kinase A signaling;cell differentiation;regulation of cAMP-mediated signaling;regulation of sperm capacitation
• Cellular component: acrosomal vesicle;integral component of membrane;sperm flagellum;sperm midpiece