TMEM179B

transmembrane protein 179B, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 11:62787402-62790400

Links

ENSG00000185475 ∙ NCBI:374395 ∙ ∙ HGNC:33744 ∙ Uniprot:Q7Z7N9 ∙ 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 TMEM179B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM179B 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			15			15
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	0

Variants in TMEM179B

This is a list of pathogenic ClinVar variants found in the TMEM179B region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62787453-C-A		not specified	Uncertain significance (Jun 06, 2023)
11-62787462-C-G		not specified	Uncertain significance (Aug 12, 2021)
11-62787465-G-C		not specified	Uncertain significance (Nov 15, 2023)
11-62787468-C-G		not specified	Uncertain significance (Dec 13, 2022)
11-62787487-T-C		not specified	Uncertain significance (May 16, 2024)
11-62787501-G-A		not specified	Uncertain significance (Mar 20, 2024)
11-62789095-C-T		not specified	Uncertain significance (Aug 26, 2022)
11-62789195-T-C		not specified	Uncertain significance (Oct 24, 2023)
11-62789197-G-A		not specified	Uncertain significance (Mar 19, 2024)
11-62789293-G-C		not specified	Uncertain significance (Nov 05, 2021)
11-62789311-A-G		not specified	Uncertain significance (Mar 11, 2022)
11-62789339-T-C		not specified	Uncertain significance (May 10, 2024)
11-62789633-C-T		not specified	Uncertain significance (Mar 23, 2022)
11-62789642-C-G		not specified	Uncertain significance (Oct 03, 2022)
11-62789662-A-G		not specified	Uncertain significance (Jul 12, 2023)
11-62789896-G-C		not specified	Uncertain significance (Nov 27, 2023)
11-62789904-T-A		not specified	Uncertain significance (Jan 18, 2023)
11-62789936-G-C		not specified	Uncertain significance (Feb 15, 2023)
11-62790031-G-A		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM179B	protein_coding	protein_coding	ENST00000333449	5	2991

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000989	0.828	125660	1	87	125748	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.843	145	119	1.22	0.00000615	1364
Missense in Polyphen		46	36.597	1.2569		484
Synonymous	-0.617	57	51.4	1.11	0.00000255	488
Loss of Function	1.17	6	10.0	0.599	4.93e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00239	0.00238
East Asian	0.00	0.00
Finnish	0.00120	0.00120
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.00	0.00
South Asian	0.000523	0.000490
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0826

Intolerance Scores

• loftool: 0.489
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.144
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem179b

Gene ontology

• Biological process: neutrophil degranulation
• Cellular component: nucleolus;plasma membrane;integral component of membrane;nuclear speck;secretory granule membrane;azurophil granule membrane;ficolin-1-rich granule membrane