TCHP

trichoplein keratin filament binding

Basic information

Region (hg38): 12:109900263-109983841

Links

ENSG00000139437 ∙ NCBI:84260 ∙ OMIM:612654 ∙ HGNC:28135 ∙ Uniprot:Q9BT92 ∙ 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 TCHP gene.

• Inborn genetic diseases (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCHP 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in TCHP

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

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

Position	Type	Phenotype	Significance	ClinVar
12-109903031-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-109903037-C-T		not specified	Uncertain significance (Oct 17, 2023)
12-109903079-A-G		not specified	Uncertain significance (May 24, 2023)
12-109903091-G-A		not specified	Uncertain significance (Aug 17, 2022)
12-109903941-C-T		not specified	Uncertain significance (Oct 29, 2021)
12-109903942-A-T		not specified	Uncertain significance (Mar 24, 2023)
12-109904762-A-G		not specified	Uncertain significance (Oct 29, 2021)
12-109904768-A-T		not specified	Uncertain significance (Sep 22, 2022)
12-109907689-A-G		not specified	Uncertain significance (Aug 13, 2021)
12-109908587-C-T		not specified	Uncertain significance (Dec 17, 2023)
12-109908697-G-C		not specified	Uncertain significance (Jan 10, 2022)
12-109908872-C-T		not specified	Uncertain significance (Jan 03, 2024)
12-109908890-T-G		not specified	Uncertain significance (Apr 25, 2022)
12-109908917-C-G		not specified	Uncertain significance (Dec 05, 2022)
12-109908922-G-T		not specified	Uncertain significance (Aug 30, 2021)
12-109911075-C-T		not specified	Uncertain significance (Dec 11, 2023)
12-109911076-G-A		not specified	Uncertain significance (Mar 14, 2023)
12-109911099-A-G		not specified	Uncertain significance (Jan 31, 2022)
12-109911104-G-C		not specified	Uncertain significance (Jan 31, 2022)
12-109911124-A-G		not specified	Uncertain significance (Mar 24, 2023)
12-109911202-G-A		not specified	Uncertain significance (May 06, 2022)
12-109911205-C-T		not specified	Uncertain significance (Nov 15, 2023)
12-109913044-G-C		not specified	Uncertain significance (Feb 15, 2023)
12-109913049-G-A		not specified	Uncertain significance (Aug 16, 2021)
12-109914457-C-G		not specified	Uncertain significance (Dec 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCHP	protein_coding	protein_coding	ENST00000312777	12	83578

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.80e-16	0.312	125365	0	383	125748	0.00152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.220	286	297	0.964	0.0000194	3236
Missense in Polyphen		83	88.991	0.93268		990
Synonymous	0.485	103	109	0.941	0.00000642	862
Loss of Function	1.47	30	40.0	0.750	0.00000243	382

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00518	0.00515
Ashkenazi Jewish	0.00189	0.00179
East Asian	0.000599	0.000598
Finnish	0.000930	0.000878
European (Non-Finnish)	0.00165	0.00163
Middle Eastern	0.000599	0.000598
South Asian	0.000489	0.000457
Other	0.00197	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tumor suppressor which has the ability to inhibit cell growth and be pro-apoptotic during cell stress. Inhibits cell growth in bladder and prostate cancer cells by a down-regulation of HSPB1 by inhibiting its phosphorylation. May act as a 'capping' or 'branching' protein for keratin filaments in the cell periphery. May regulate K8/K18 filament and desmosome organization mainly at the apical or peripheral regions of simple epithelial cells (PubMed:15731013, PubMed:18931701). Is a negative regulator of ciliogenesis (PubMed:25270598). {ECO:0000269|PubMed:15731013, ECO:0000269|PubMed:18931701, ECO:0000269|PubMed:25270598}.

Recessive Scores

• pRec: 0.559

Intolerance Scores

• loftool: 0.997
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.7

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.486
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.729

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tchp
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: apoptotic process;cell projection organization;negative regulation of cell growth;negative regulation of cilium assembly
• Cellular component: cytoplasm;mitochondrion;centrosome;cytosol;plasma membrane;desmosome;keratin filament;apical cortex
• Molecular function: protein binding