TMEM52

transmembrane protein 52

Basic information

Region (hg38): 1:1917590-1919279

Links

ENSG00000178821 ∙ NCBI:339456 ∙ ∙ HGNC:27916 ∙ Uniprot:Q8NDY8 ∙ 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 TMEM52 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM52 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	0

Variants in TMEM52

This is a list of pathogenic ClinVar variants found in the TMEM52 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-1917896-G-A		not specified	Uncertain significance (Aug 14, 2024)
1-1917916-G-A		not specified	Uncertain significance (Dec 09, 2023)
1-1917947-T-C		not specified	Uncertain significance (Nov 19, 2022)
1-1917956-G-C		not specified	Uncertain significance (Oct 05, 2023)
1-1917995-G-A		not specified	Uncertain significance (Dec 14, 2023)
1-1918005-T-G		not specified	Uncertain significance (Nov 14, 2023)
1-1918010-C-T		not specified	Uncertain significance (Aug 21, 2024)
1-1918040-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-1918070-G-T		not specified	Uncertain significance (Oct 30, 2023)
1-1918093-G-A		not specified	Uncertain significance (Jan 07, 2022)
1-1918151-C-T		not specified	Uncertain significance (Nov 10, 2024)
1-1918278-G-C		not specified	Uncertain significance (Mar 01, 2024)
1-1918288-A-C		not specified	Uncertain significance (Jun 18, 2021)
1-1918304-C-T		not specified	Uncertain significance (Jan 31, 2024)
1-1918318-C-T		not specified	Uncertain significance (Apr 05, 2023)
1-1918348-G-T		not specified	Uncertain significance (Nov 13, 2024)
1-1918349-C-T		not specified	Uncertain significance (Nov 13, 2024)
1-1918358-G-A		not specified	Uncertain significance (Mar 01, 2025)
1-1918385-C-G		not specified	Uncertain significance (Feb 07, 2025)
1-1918417-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-1918897-C-A		not specified	Uncertain significance (Nov 21, 2022)
1-1918918-G-A		not specified	Uncertain significance (Feb 17, 2024)
1-1918920-G-A		not specified	Uncertain significance (Oct 08, 2024)
1-1919067-C-A		not specified	Uncertain significance (Jun 21, 2022)
1-1919208-G-A		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM52	protein_coding	protein_coding	ENST00000310991	5	1684

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0149	0.704	125187	1	71	125259	0.000287

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.384	114	103	1.11	0.00000596	1295
Missense in Polyphen		35	34.889	1.0032		488
Synonymous	-0.849	52	44.8	1.16	0.00000268	480
Loss of Function	0.646	3	4.47	0.671	1.92e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000916	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00223	0.00219
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.409
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.0832
• hipred: N
• hipred_score: 0.146
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.110

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Tmem52

Gene ontology

• Cellular component: integral component of membrane