TMEM9B

TMEM9 domain family member B

Basic information

Region (hg38): 11:8947201-8965011

Previous symbols: [ "C11orf15" ]

Links

ENSG00000175348 ∙ NCBI:56674 ∙ OMIM:620293 ∙ HGNC:1168 ∙ Uniprot:Q9NQ34 ∙ 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 TMEM9B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM9B 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in TMEM9B

This is a list of pathogenic ClinVar variants found in the TMEM9B region.

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

Position	Type	Phenotype	Significance	ClinVar
11-8948415-C-T		not specified	Uncertain significance (Feb 28, 2024)
11-8948448-C-T		not specified	Uncertain significance (Oct 10, 2023)
11-8953226-T-G		not specified	Uncertain significance (Jan 09, 2024)
11-8956213-C-G		not specified	Uncertain significance (Aug 16, 2022)
11-8956234-G-A		not specified	Uncertain significance (Dec 07, 2023)
11-8964218-G-T		not specified	Uncertain significance (Sep 14, 2022)
11-8964219-T-A		not specified	Uncertain significance (Jul 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM9B	protein_coding	protein_coding	ENST00000534025	5	17718

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.531	0.466	125734	0	7	125741	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	78	113	0.691	0.00000634	1270
Missense in Polyphen		20	37.152	0.53833		422
Synonymous	0.178	40	41.5	0.965	0.00000206	397
Loss of Function	2.47	2	10.7	0.187	6.04e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000603	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000558	0.0000527
Middle Eastern	0.0000603	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhances production of proinflammatory cytokines induced by TNF, IL1B, and TLR ligands. Has a role in TNF activation of both the NF-kappaB and MAPK pathways. {ECO:0000269|PubMed:18541524}.

Recessive Scores

• pRec: 0.0653

Intolerance Scores

• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.115
• hipred: Y
• hipred_score: 0.531
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.452

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem9b

Gene ontology

• Biological process: positive regulation of I-kappaB kinase/NF-kappaB signaling
• Cellular component: lysosomal membrane;integral component of membrane;early endosome membrane