TPD52L1

TPD52 like 1

Basic information

Region (hg38): 6:125119048-125264407

Links

ENSG00000111907 ∙ ∙ OMIM:604069 ∙ HGNC:12006 ∙ Uniprot:Q16890 ∙ 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 TPD52L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPD52L1 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in TPD52L1

This is a list of pathogenic ClinVar variants found in the TPD52L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-125220143-A-G		not specified	Uncertain significance (Jun 05, 2024)
6-125220147-T-C		not specified	Uncertain significance (Jun 28, 2023)
6-125229180-G-C		not specified	Uncertain significance (Jan 10, 2022)
6-125248344-A-G		not specified	Uncertain significance (Mar 21, 2023)
6-125262846-G-A		not specified	Uncertain significance (Sep 29, 2023)
6-125262850-C-T		not specified	Uncertain significance (Mar 21, 2023)
6-125262882-C-G		not specified	Uncertain significance (Nov 12, 2021)
6-125262951-C-G		not specified	Uncertain significance (Jun 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPD52L1	protein_coding	protein_coding	ENST00000534000	7	145359

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000149	0.662	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	85	119	0.714	0.00000685	1354
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000727	0.000726
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.000167	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.944
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.309
• hipred: N
• hipred_score: 0.387
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tpd52l1

Gene ontology

• 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
• Cellular component: cytoplasm;perinuclear region of cytoplasm
• Molecular function: protein binding;identical protein binding;protein homodimerization activity;protein heterodimerization activity