TMEM119

transmembrane protein 119

Basic information

Region (hg38): 12:108589851-108598320

Links

ENSG00000183160 ∙ NCBI:338773 ∙ OMIM:618989 ∙ HGNC:27884 ∙ Uniprot:Q4V9L6 ∙ 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 TMEM119 gene.

• not_specified (58 variants)
• not_provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM119 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000181724.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			51	8	1	60
nonsense					1	1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	8	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM119	protein_coding	protein_coding	ENST00000392806	1	8475

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.625	0.347	124501	0	5	124506	0.0000201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.294	170	181	0.938	0.0000111	1779
Missense in Polyphen		51	60.449	0.84368		602
Synonymous	-0.970	102	90.3	1.13	0.00000649	635
Loss of Function	1.64	0	3.13	0.00	1.34e-7	34

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000124
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000479	0.0000462
European (Non-Finnish)	0.0000189	0.0000179
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in bone formation and normal bone mineralization. Promotes the differentiation of myoblasts into osteoblasts (PubMed:20025746). May induce the commitment and differentiation of myoblasts into osteoblasts through an enhancement of BMP2 production and interaction with the BMP-RUNX2 pathway. Upregulates the expression of ATF4, a transcription factor which plays a central role in osteoblast differentiation. Essential for normal spermatogenesis and late testicular differentiation (By similarity). {ECO:0000250|UniProtKB:Q8R138, ECO:0000269|PubMed:20025746}.

Intolerance Scores

• loftool: 0.752
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.146
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem119
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype

Gene ontology

• Biological process: osteoblast differentiation;spermatogenesis;positive regulation of bone mineralization;biomineral tissue development;positive regulation of osteoblast proliferation;positive regulation of osteoblast differentiation;spermatid differentiation;positive regulation of bone development
• Cellular component: endoplasmic reticulum membrane;plasma membrane;integral component of membrane
• Molecular function: molecular_function