TMEM119

transmembrane protein 119

Basic information

Region (hg38): 12:108589850-108598320

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.

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.

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			17	5	1	23
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	5	3

Variants in TMEM119

This is a list of pathogenic ClinVar variants found in the TMEM119 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-108591543-G-A		not specified	Uncertain significance (Nov 19, 2022)
12-108591578-G-A		not specified	Uncertain significance (Dec 06, 2022)
12-108591624-C-T		not specified	Uncertain significance (Nov 17, 2022)
12-108591692-G-A		not specified	Likely benign (Oct 12, 2021)
12-108591693-C-A		not specified	Uncertain significance (Feb 17, 2024)
12-108591694-C-A		not specified	Uncertain significance (May 07, 2024)
12-108591710-G-A		not specified	Uncertain significance (Feb 27, 2023)
12-108591759-C-T		not specified	Uncertain significance (Jan 03, 2024)
12-108591807-C-T		not specified	Likely benign (Feb 06, 2024)
12-108591873-G-A			Benign (Jul 06, 2018)
12-108591875-C-T		not specified	Likely benign (Mar 20, 2023)
12-108591896-T-A		not specified	Uncertain significance (Sep 26, 2022)
12-108591915-C-G		not specified	Uncertain significance (Jun 03, 2022)
12-108591931-A-G			Benign (Mar 30, 2018)
12-108591936-A-C		not specified	Uncertain significance (Jun 11, 2021)
12-108591951-C-T		not specified	Uncertain significance (Jun 07, 2024)
12-108591995-G-A		not specified	Uncertain significance (Sep 12, 2023)
12-108592002-A-G		not specified	Uncertain significance (Mar 22, 2023)
12-108592040-G-A		not specified	Uncertain significance (Mar 06, 2023)
12-108592096-C-T		not specified	Uncertain significance (May 03, 2023)
12-108592241-G-A			Benign (Feb 20, 2018)
12-108592263-T-C		not specified	Uncertain significance (Jan 18, 2022)
12-108592268-G-A			Likely benign (Apr 01, 2023)
12-108592272-C-T		not specified	Likely benign (Feb 06, 2023)
12-108592301-A-C		not specified	Uncertain significance (Dec 07, 2021)

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