TMEM176B

transmembrane protein 176B, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 7:150791285-150801360

Links

ENSG00000106565 ∙ NCBI:28959 ∙ OMIM:610385 ∙ HGNC:29596 ∙ Uniprot:Q3YBM2 ∙ 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 TMEM176B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM176B 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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in TMEM176B

This is a list of pathogenic ClinVar variants found in the TMEM176B region.

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

Position	Type	Phenotype	Significance	ClinVar
7-150791568-G-T		not specified	Uncertain significance (Dec 11, 2024)
7-150792077-A-C		not specified	Uncertain significance (Jun 04, 2024)
7-150792126-T-C		not specified	Uncertain significance (Mar 17, 2023)
7-150792156-C-A		not specified	Uncertain significance (May 15, 2023)
7-150792157-G-A		not specified	Likely benign (Sep 27, 2022)
7-150792157-G-T		not specified	Uncertain significance (Sep 27, 2021)
7-150792159-A-G		not specified	Uncertain significance (Aug 26, 2024)
7-150793095-A-G		not specified	Uncertain significance (Feb 23, 2023)
7-150793102-T-A		not specified	Uncertain significance (Feb 11, 2022)
7-150793125-T-G		not specified	Uncertain significance (Jan 30, 2024)
7-150793146-C-T		not specified	Likely benign (Feb 15, 2023)
7-150793168-T-C		not specified	Uncertain significance (Nov 09, 2023)
7-150793257-A-G		not specified	Uncertain significance (May 26, 2022)
7-150793995-C-T		not specified	Uncertain significance (Dec 21, 2022)
7-150794052-C-T		not specified	Uncertain significance (Mar 22, 2022)
7-150794067-G-C		not specified	Uncertain significance (Dec 23, 2024)
7-150796403-G-A		not specified	Uncertain significance (Nov 12, 2024)
7-150796413-T-C		not specified	Uncertain significance (Jan 07, 2022)
7-150796415-T-A		not specified	Uncertain significance (Nov 09, 2021)
7-150796418-C-T		not specified	Uncertain significance (Oct 03, 2022)
7-150796436-T-C		not specified	Uncertain significance (Nov 15, 2021)
7-150796499-T-G		not specified	Uncertain significance (Jun 02, 2023)
7-150796535-G-A		not specified	Uncertain significance (Jun 24, 2022)
7-150796542-C-T		not specified	Uncertain significance (Oct 03, 2022)
7-150796565-G-A		not specified	Uncertain significance (Feb 12, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM176B	protein_coding	protein_coding	ENST00000447204	6	10076

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.42e-10	0.0297	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.231	155	147	1.05	0.00000765	1699
Missense in Polyphen		34	35.237	0.96491		470
Synonymous	-0.872	71	62.2	1.14	0.00000352	575
Loss of Function	-0.521	14	12.1	1.16	5.99e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000893	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000328	0.0000327
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the process of maturation of dendritic cells. Required for the development of cerebellar granule cells (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0981

Intolerance Scores

• loftool: 0.978
• rvis_EVS: 1.24
• rvis_percentile_EVS: 93.39

Haploinsufficiency Scores

• pHI: 0.0510
• hipred: N
• hipred_score: 0.139

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	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tmem176b
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: animal organ morphogenesis;cell differentiation;negative regulation of dendritic cell differentiation
• Cellular component: integral component of membrane;nuclear membrane