TMEM219

transmembrane protein 219

Basic information

Region (hg38): 16:29940885-29973050

Links

ENSG00000149932 ∙ NCBI:124446 ∙ OMIM:620290 ∙ HGNC:25201 ∙ Uniprot:Q86XT9 ∙ 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 TMEM219 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM219 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					1	1
missense			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	2

Variants in TMEM219

This is a list of pathogenic ClinVar variants found in the TMEM219 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-29963169-A-T		not specified	Uncertain significance (Sep 13, 2023)
16-29963289-G-A		not specified	Uncertain significance (Aug 13, 2021)
16-29963421-T-A		not specified	Uncertain significance (Jul 25, 2023)
16-29963426-T-C			Benign (Jul 06, 2018)
16-29963437-C-A		not specified	Uncertain significance (Feb 22, 2024)
16-29963464-C-T		not specified	Uncertain significance (Oct 25, 2022)
16-29963544-C-T		not specified	Uncertain significance (Jun 27, 2022)
16-29968051-A-G		not specified	Uncertain significance (Sep 08, 2023)
16-29968109-T-C			Benign (Jul 06, 2018)
16-29968141-A-G		not specified	Uncertain significance (Jun 02, 2023)
16-29968171-G-A		not specified	Uncertain significance (Sep 26, 2022)
16-29968210-G-T		not specified	Uncertain significance (Aug 04, 2021)
16-29971435-C-A		not specified	Uncertain significance (Jul 08, 2022)
16-29971508-C-G		not specified	Uncertain significance (Mar 19, 2024)
16-29971508-C-T		not specified	Uncertain significance (Dec 06, 2022)
16-29971510-C-T		not specified	Uncertain significance (Dec 11, 2023)
16-29971513-C-T		not specified	Uncertain significance (Aug 16, 2022)
16-29971514-G-A		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM219	protein_coding	protein_coding	ENST00000566848	4	32168

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000817	0.547	124772	0	25	124797	0.000100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.242	126	134	0.941	0.00000723	1516
Missense in Polyphen		43	44.603	0.96407		533
Synonymous	0.441	53	57.2	0.926	0.00000293	554
Loss of Function	0.579	7	8.86	0.790	4.61e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000346	0.000345
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.000334	0.000334
Finnish	0.00	0.00
European (Non-Finnish)	0.0000445	0.0000441
Middle Eastern	0.000334	0.000334
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell death receptor specific for IGFBP3, may mediate caspase-8-dependent apoptosis upon ligand binding. {ECO:0000269|PubMed:20353938}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;Transcriptional Regulation by TP53;TP53 Regulates Transcription of Death Receptors and Ligands (Consensus)

Intolerance Scores

• loftool: 0.322
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.248
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.120

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem219
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; neoplasm; respiratory system phenotype; immune system phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: apoptotic process;regulation of apoptotic process
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding