TMEM52B

transmembrane protein 52B

Basic information

Region (hg38): 12:10170541-10191804

Previous symbols: [ "C12orf59" ]

Links

ENSG00000165685 ∙ NCBI:120939 ∙ ∙ HGNC:26438 ∙ Uniprot:Q4KMG9 ∙ 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 TMEM52B gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM52B 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 TMEM52B

This is a list of pathogenic ClinVar variants found in the TMEM52B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10172034-G-A		not specified	Uncertain significance (Dec 03, 2021)
12-10179610-C-G		not specified	Uncertain significance (Oct 30, 2023)
12-10186497-G-A		not specified	Uncertain significance (Aug 12, 2021)
12-10186521-G-C		not specified	Uncertain significance (Sep 27, 2021)
12-10186542-C-A		not specified	Uncertain significance (Mar 07, 2024)
12-10186556-G-A		not specified	Uncertain significance (Apr 20, 2023)
12-10186562-G-A		not specified	Uncertain significance (Dec 28, 2023)
12-10189926-G-A		not specified	Uncertain significance (Feb 23, 2023)
12-10189958-T-A		not specified	Uncertain significance (Jun 01, 2022)
12-10189988-A-G		not specified	Uncertain significance (Nov 14, 2023)
12-10190045-G-A		not specified	Uncertain significance (Nov 12, 2021)
12-10190099-A-G		not specified	Uncertain significance (Aug 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM52B	protein_coding	protein_coding	ENST00000298530	4	21260

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00107	0.622	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.311	106	97.4	1.09	0.00000564	1037
Missense in Polyphen		31	35.874	0.86412		358
Synonymous	0.471	37	40.8	0.906	0.00000256	344
Loss of Function	0.568	5	6.57	0.761	2.81e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000334	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• pHI: 0.284
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem52b

Gene ontology

• Biological process: biological_process
• Cellular component: integral component of membrane;extracellular exosome
• Molecular function: molecular_function