GeneBe

TCHP

trichoplein keratin filament binding

Basic information

Region (hg38): 12:109900264-109983841

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.

  • not_specified (64 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. These statistics are base on transcript: NM_001143852.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
63
clinvar
1
clinvar
 64
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 63 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TCHPprotein_codingprotein_codingENST00000312777 1283578
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.80e-160.31212536503831257480.00152
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2202862970.9640.00001943236
Missense in Polyphen8388.9910.93268990
Synonymous0.4851031090.9410.00000642862
Loss of Function1.473040.00.7500.00000243382

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.005180.00515
Ashkenazi Jewish0.001890.00179
East Asian0.0005990.000598
Finnish0.0009300.000878
European (Non-Finnish)0.001650.00163
Middle Eastern0.0005990.000598
South Asian0.0004890.000457
Other0.001970.00196

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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