TCHP

protein-coding

trichoplein keratin filament binding

Gene summary

Involved in apoptotic process; negative regulation of cell growth; and negative regulation of cilium assembly. Located in several cellular components, including apical cortex; cytoskeleton; and mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001143852.2

Inheritance

—

ClinVar variants

U:82B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr12:109,900,264-109,983,841

External References & Databases

Ensembl (ENSG00000139437)

Transcript & Mutation Effects

hg38 • Region Span ~83.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TCHP variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 74

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001143852.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar			3
missense			74 clinvar	1 clinvar		75
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	82	1	0	83

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001143852.2	RefSeq	NP_001137324.1	12	MANE Select
ENST00000405876.9	Ensembl	ENSP00000384520.4	12	MANE Select
NM_032300.5	RefSeq	NP_115676.1	12	Standard
ENST00000312777.10	Ensembl	ENSP00000324404.5	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

apoptotic process
cell projection organization
negative regulation of cell growth
negative regulation of cilium assembly

Molecular Function

protein binding

Cellular Component

cytoplasm
mitochondrion
centrosome
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000312777
Coding exons: 12
Length: 83578
Individuals with no LoFs: 125365
Homozygous LoFs: 0
Heterozygous LoFs: 383
Defined: 125748
p: 0.00152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.220	286	297	0.964	0.0000194	3236
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0029	0.0029	notable
Latino/Admixed American	0.0022	0.0022	notable
Ashkenazi Jewish	0.0019	0.0018	notable
East Asian	0.00060	0.00060	rare
Finnish	0.00093	0.00088	rare
European (Non-Finnish)	0.0016	0.0016	notable
South Asian	0.00049	0.00046	rare
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.729

Gene Damage Prediction

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