TMEM50B

transmembrane protein 50B

Basic information

Region (hg38): 21:33432484-33479974

Previous symbols: [ "C21orf4" ]

Links

ENSG00000142188 ∙ NCBI:757 ∙ OMIM:617894 ∙ HGNC:1280 ∙ Uniprot:P56557 ∙ 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 TMEM50B gene.

• Immunodeficiency 28 (58 variants)
• not provided (18 variants)
• Inborn genetic diseases (8 variants)
• not specified (4 variants)
• Interferon gamma receptor deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM50B 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding			27	23	10	60
Total	0	0	33	24	10

Variants in TMEM50B

This is a list of pathogenic ClinVar variants found in the TMEM50B region.

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

Position	Type	Phenotype	Significance	ClinVar
21-33432509-A-C			not provided (-)
21-33432623-A-T			not provided (-)
21-33432659-T-C		not specified	Benign (Jan 24, 2024)
21-33432672-C-T			not provided (-)
21-33432704-C-T		Immunodeficiency 28	Likely benign (Apr 07, 2023)
21-33432706-C-G		Immunodeficiency 28	Likely benign (Sep 01, 2023)
21-33432716-T-A		Immunodeficiency 28	Uncertain significance (Aug 30, 2021)
21-33432729-A-G		Inborn genetic diseases	Uncertain significance (Nov 28, 2023)
21-33432748-C-T		Immunodeficiency 28 • IFNGR2-related disorder	Likely benign (Oct 16, 2023)
21-33432749-G-A		Immunodeficiency 28	Uncertain significance (Aug 23, 2022)
21-33432753-G-A		Immunodeficiency 28	Uncertain significance (Jul 12, 2022)
21-33432753-G-T		Immunodeficiency 28	Uncertain significance (Apr 01, 2022)
21-33432756-C-T		Immunodeficiency 28	Uncertain significance (Sep 01, 2022)
21-33432760-T-C		Immunodeficiency 28	Likely benign (Jun 12, 2022)
21-33432763-G-A		Immunodeficiency 28	Likely benign (Dec 25, 2023)
21-33432766-G-A		Immunodeficiency 28	Likely benign (Dec 05, 2022)
21-33432771-C-T		Immunodeficiency 28	Likely benign (Jan 29, 2024)
21-33432772-G-A		Immunodeficiency 28	Likely benign (Feb 21, 2023)
21-33432772-G-C		Immunodeficiency 28	Likely benign (Jan 10, 2023)
21-33432772-G-T			not provided (-)
21-33432778-G-A		Immunodeficiency 28	Likely benign (Jan 07, 2023)
21-33432780-C-T		Immunodeficiency 28	Uncertain significance (Feb 06, 2023)
21-33432783-G-A		Immunodeficiency 28	Uncertain significance (Feb 01, 2022)
21-33432787-C-T		Immunodeficiency 28	Likely benign (May 29, 2020)
21-33432789-GT-G		Immunodeficiency 28	Likely pathogenic (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM50B	protein_coding	protein_coding	ENST00000542230	6	47527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0294	0.928	125717	0	27	125744	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.875	64	87.0	0.736	0.00000423	1045
Missense in Polyphen		16	26.377	0.6066		332
Synonymous	-0.527	33	29.4	1.12	0.00000158	292
Loss of Function	1.75	4	9.95	0.402	4.84e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000612	0.000612
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.498
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.444
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem50b

Gene ontology

• Biological process: biological_process;late endosome to vacuole transport via multivesicular body sorting pathway
• Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of membrane
• Molecular function: molecular_function