TMEM139

transmembrane protein 139

Basic information

Region (hg38): 7:143279957-143288048

Links

ENSG00000178826 ∙ NCBI:135932 ∙ OMIM:616524 ∙ HGNC:22058 ∙ Uniprot:Q8IV31 ∙ 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 TMEM139 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM139 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			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in TMEM139

This is a list of pathogenic ClinVar variants found in the TMEM139 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-143285995-C-T		not specified	Uncertain significance (Nov 03, 2022)
7-143286055-C-T		not specified	Uncertain significance (Apr 12, 2023)
7-143286104-C-G		not specified	Uncertain significance (Jan 08, 2024)
7-143286140-G-C		not specified	Likely benign (Jul 12, 2023)
7-143286151-C-G		not specified	Uncertain significance (Feb 07, 2023)
7-143286180-C-G		not specified	Uncertain significance (Oct 12, 2022)
7-143286202-G-A			Likely benign (Nov 01, 2022)
7-143286515-C-A		not specified	Uncertain significance (Aug 17, 2022)
7-143286588-C-A		not specified	Uncertain significance (Aug 17, 2022)
7-143286593-C-G		not specified	Uncertain significance (Aug 17, 2021)
7-143286669-G-A		not specified	Uncertain significance (Sep 01, 2021)
7-143286683-C-T		not specified	Uncertain significance (Jan 24, 2023)
7-143286720-C-T		not specified	Uncertain significance (Nov 06, 2023)
7-143286787-T-G		not specified	Uncertain significance (Jun 05, 2023)
7-143286801-T-C		not specified	Uncertain significance (Apr 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM139	protein_coding	protein_coding	ENST00000359333	2	8092

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00755	0.791	125721	0	23	125744	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.214	130	123	1.05	0.00000689	1368
Missense in Polyphen		35	31.689	1.1045		356
Synonymous	0.437	47	51.0	0.922	0.00000276	476
Loss of Function	0.981	4	6.75	0.593	3.72e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000136	0.000132
Middle Eastern	0.00	0.00
South Asian	0.0000992	0.0000980
Other	0.000197	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in cellular trafficking of proteins such as SLC4A1. {ECO:0000305|PubMed:26049106}.

Recessive Scores

• pRec: 0.0402

Intolerance Scores

• loftool: 0.398
• rvis_EVS: 0.7
• rvis_percentile_EVS: 85.42

Haploinsufficiency Scores

• pHI: 0.00814
• hipred: N
• hipred_score: 0.123
• ghis: 0.364

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00938

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem139

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding