TMEM9B

protein-coding

TMEM9 domain family member B

Gene summary

Involved in positive regulation of canonical NF-kappaB signal transduction. Located in early endosome membrane and lysosomal membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C11orf15

MANE transcript

NM_020644.3

Inheritance

—

ClinVar variants

U:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr11:8,947,202-8,965,011

External References & Databases

Ensembl (ENSG00000175348)

Transcript & Mutation Effects

hg38 • Region Span ~17.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMEM9B variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020644.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			14 clinvar			14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	16	0	0	16

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020644.3	RefSeq	NP_065695.1	5	MANE Select
ENST00000534025.6	Ensembl	ENSP00000433361.1	5	MANE Select
NM_001286094.2	RefSeq	NP_001273023.1	3	Standard
NM_001286095.2	RefSeq	NP_001273024.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of I-kappaB kinase/NF-kappaB signaling

Cellular Component

lysosomal membrane
integral component of membrane
early endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000534025
Coding exons: 5
Length: 17718
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125741
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.17	78	113	0.691	0.00000634	1270
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000060	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000056	0.000053	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.452

Gene Damage Prediction

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