TPD52L3

TPD52 like 3

Basic information

Region (hg38): 9:6328375-6331891

Links

ENSG00000170777 ∙ NCBI:89882 ∙ OMIM:617567 ∙ HGNC:23382 ∙ Uniprot:Q96J77 ∙ 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 TPD52L3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPD52L3 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			13	1		14
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	14	1	0

Variants in TPD52L3

This is a list of pathogenic ClinVar variants found in the TPD52L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-6328624-T-A		not specified	Uncertain significance (Sep 07, 2022)
9-6328639-C-T		not specified	Uncertain significance (Jul 19, 2023)
9-6328643-C-G		not specified	Uncertain significance (Feb 22, 2025)
9-6328707-A-G		not specified	Uncertain significance (Jul 30, 2024)
9-6328734-C-T		not specified	Uncertain significance (Feb 08, 2025)
9-6328755-G-A		not specified	Uncertain significance (Nov 21, 2024)
9-6328762-G-A		not specified	Uncertain significance (Feb 28, 2023)
9-6328783-A-G		not specified	Uncertain significance (Oct 02, 2023)
9-6328802-G-T		not specified	Uncertain significance (Apr 20, 2024)
9-6328856-C-G		not specified	Uncertain significance (Jan 23, 2024)
9-6328873-A-G		not specified	Uncertain significance (Aug 28, 2024)
9-6328875-A-C		not specified	Uncertain significance (Dec 15, 2023)
9-6328897-T-C		not specified	Uncertain significance (Jan 03, 2024)
9-6328918-A-G		not specified	Uncertain significance (Jul 15, 2021)
9-6328929-G-A		not specified	Likely benign (Feb 17, 2022)
9-6328954-C-A		not specified	Uncertain significance (Feb 27, 2023)
9-6329011-G-C		not specified	Uncertain significance (Jul 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPD52L3	protein_coding	protein_coding	ENST00000344545	1	3552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.198	0.659	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.23	103	73.4	1.40	0.00000412	883
Missense in Polyphen		26	15.843	1.6412		251
Synonymous	0.112	30	30.8	0.974	0.00000168	302
Loss of Function	0.976	1	2.75	0.364	1.19e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0579

Intolerance Scores

• loftool: 0.858
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.0203
• hipred: N
• hipred_score: 0.112
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.347

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trpd52l3

Gene ontology

• Molecular function: protein binding