TMEM50A

transmembrane protein 50A

Basic information

Region (hg38): 1:25338317-25362361

Links

ENSG00000183726 ∙ NCBI:23585 ∙ OMIM:605348 ∙ HGNC:30590 ∙ Uniprot:O95807 ∙ 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 TMEM50A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM50A 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in TMEM50A

This is a list of pathogenic ClinVar variants found in the TMEM50A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-25340533-G-T		not specified	Uncertain significance (Oct 06, 2024)
1-25340554-T-C		not specified	Uncertain significance (May 06, 2024)
1-25352888-G-A		not specified	Uncertain significance (Jul 08, 2022)
1-25352900-T-A		not specified	Uncertain significance (Feb 07, 2025)
1-25352942-T-C		not specified	Uncertain significance (Feb 12, 2025)
1-25352947-A-G		not specified	Uncertain significance (Nov 08, 2021)
1-25360668-T-G		not specified	Uncertain significance (Nov 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM50A	protein_coding	protein_coding	ENST00000374358	6	24445

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.163	0.824	125731	0	11	125742	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.702	69	87.5	0.789	0.00000435	1024
Missense in Polyphen		21	34.281	0.61258		384
Synonymous	1.12	20	27.4	0.729	0.00000131	294
Loss of Function	2.13	3	10.4	0.287	5.29e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000553	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000553	0.0000544
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.581
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.342
• hipred: N
• hipred_score: 0.444
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem50a

Gene ontology

• Biological process: late endosome to vacuole transport via multivesicular body sorting pathway
• Cellular component: endoplasmic reticulum;integral component of membrane;neuronal cell body;glial cell projection