TPD52L2

TPD52 like 2

Basic information

Region (hg38): 20:63865228-63891545

Links

ENSG00000101150 ∙ NCBI:7165 ∙ OMIM:603747 ∙ HGNC:12007 ∙ Uniprot:O43399 ∙ 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 TPD52L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPD52L2 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			10	2	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	11	2	1

Variants in TPD52L2

This is a list of pathogenic ClinVar variants found in the TPD52L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63865376-C-A		not specified	Uncertain significance (Jun 17, 2024)
20-63869344-C-T		not specified	Uncertain significance (Nov 17, 2022)
20-63869374-C-T		not specified	Uncertain significance (Jan 26, 2022)
20-63869376-C-T		not specified	Uncertain significance (Dec 16, 2023)
20-63873692-C-T		not specified	Uncertain significance (Jan 09, 2024)
20-63873800-G-A			Benign (Dec 31, 2018)
20-63873813-G-A		not specified	Likely benign (Jul 09, 2021)
20-63875851-A-G		not specified	Uncertain significance (Sep 22, 2022)
20-63875863-C-A		not specified	Uncertain significance (Dec 18, 2023)
20-63886023-C-T		not specified	Uncertain significance (Feb 27, 2024)
20-63889193-C-A		not specified	Uncertain significance (Mar 28, 2023)
20-63889210-C-T		not specified	Uncertain significance (Oct 04, 2022)
20-63889222-G-A		not specified	Uncertain significance (Mar 31, 2024)
20-63889857-T-C		not specified	Uncertain significance (Aug 02, 2021)
20-63889899-C-T		not specified	Uncertain significance (Oct 03, 2022)
20-63889934-G-A		not specified	Likely benign (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPD52L2	protein_coding	protein_coding	ENST00000217121	9	26303

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000202	0.913	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00838	124	124	1.00	0.00000651	1471
Missense in Polyphen		42	44.449	0.94491		569
Synonymous	0.141	47	48.2	0.974	0.00000279	459
Loss of Function	1.55	8	14.3	0.559	7.63e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000881	0.0000881
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000140	0.000139
European (Non-Finnish)	0.0000793	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.608
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.57

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.423
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.944

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tpd52l2
• Phenotype: liver/biliary system phenotype; growth/size/body region phenotype

Gene ontology

• Molecular function: RNA binding;catalytic activity