TMEM239

transmembrane protein 239

Basic information

Region (hg38): 20:2816301-2820284

Links

ENSG00000198326 ∙ NCBI:100288797 ∙ ∙ HGNC:40044 ∙ Uniprot:Q8WW34 ∙ 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 TMEM239 gene.

• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM239 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in TMEM239

This is a list of pathogenic ClinVar variants found in the TMEM239 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-2816566-G-T		not specified	Uncertain significance (Oct 26, 2021)
20-2816571-G-A		not specified	Uncertain significance (Sep 14, 2021)
20-2816588-A-G		not specified	Uncertain significance (Jan 09, 2023)
20-2816604-G-A		not specified	Uncertain significance (Oct 06, 2021)
20-2816636-G-A		not specified	Uncertain significance (Sep 27, 2021)
20-2816640-C-T		not specified	Uncertain significance (Nov 07, 2022)
20-2816657-C-T		not specified	Uncertain significance (Mar 07, 2023)
20-2816663-T-G		not specified	Uncertain significance (Mar 11, 2024)
20-2816682-C-T		not specified	Uncertain significance (Oct 29, 2021)
20-2816733-G-A		not specified	Uncertain significance (Jul 14, 2021)
20-2816844-C-T		not specified	Uncertain significance (Dec 20, 2023)
20-2816853-G-C		not specified	Uncertain significance (Jun 24, 2022)
20-2816865-T-C		not specified	Uncertain significance (Sep 20, 2023)
20-2816892-G-C		not specified	Uncertain significance (Sep 26, 2023)
20-2816916-C-T		not specified	Uncertain significance (Apr 12, 2022)
20-2816981-C-T		not specified	Uncertain significance (Dec 13, 2023)
20-2816987-G-A		not specified	Uncertain significance (Sep 27, 2022)
20-2817002-T-G		not specified	Uncertain significance (Apr 07, 2022)
20-2817006-A-G		not specified	Uncertain significance (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM239	protein_coding	protein_coding	ENST00000380585	1	5317

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00103	0.614	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.421	76	87.1	0.873	0.00000537	943
Missense in Polyphen		32	36.161	0.88494		424
Synonymous	0.390	39	42.2	0.924	0.00000268	340
Loss of Function	0.547	5	6.51	0.768	3.71e-7	42

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.48
• rvis_percentile_EVS: 78.95

Haploinsufficiency Scores

• pHI: 0.00570
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem239

Gene ontology

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