TPD52L1

protein-coding

TPD52 like 1

Gene summary

This gene encodes a member of a family of proteins that contain coiled-coil domains and may form hetero- or homomers. The encoded protein is involved in cell proliferation and calcium signaling. It also interacts with the mitogen-activated protein kinase kinase kinase 5 (MAP3K5/ASK1) and positively regulates MAP3K5-induced apoptosis. Multiple alternatively spliced transcript variants have been observed. [provided by RefSeq, Jan 2016]

MANE transcript

NM_003287.4

Inheritance

—

ClinVar variants

U:31

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr6:125,119,049-125,264,407

External References & Databases

Ensembl (ENSG00000111907)

Transcript & Mutation Effects

hg38 • Region Span ~145.4 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 TPD52L1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 22

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003287.4. 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						0
missense			25 clinvar			25
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	31	0	0	31

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003287.4	RefSeq	NP_003278.1	7	MANE Select
ENST00000534000.6	Ensembl	ENSP00000434142.1	7	MANE Select
NM_001003395.3	RefSeq	NP_001003395.1	6	Standard
NM_001003396.3	RefSeq	NP_001003396.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Golgi Associated Vesicle Biogenesis
Clathrin derived vesicle budding
trans-Golgi Network Vesicle Budding
Vesicle-mediated transport
Membrane Trafficking

Biological Process

G2/M transition of mitotic cell cycle
positive regulation of MAP kinase activity
positive regulation of JNK cascade
positive regulation of apoptotic signaling pathway

Molecular Function

protein binding
identical protein binding
protein homodimerization activity
protein heterodimerization activity

Cellular Component

cytoplasm
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000534000
Coding exons: 7
Length: 145359
Individuals with no LoFs: 125722
Homozygous LoFs: 0
Heterozygous LoFs: 26
Defined: 125748
p: 0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.11	85	119	0.714	0.00000685	1354
Missense (PolyPhen)		33	45.202	0.73005		568
Synonymous	0.856	37	44.2	0.836	0.00000285	363
Loss of Function	0.945	9	12.6	0.713	7.21e-7	141

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000026	rare
South Asian	0.00017	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.944
RVIS EVS: 0.13
RVIS percentile EVS: 63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.860

Gene Damage Prediction

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