TMEM106A

protein-coding

transmembrane protein 106A

Gene summary

Predicted to be involved in several processes, including positive regulation of MHC class II biosynthetic process; positive regulation of cytokine production; and positive regulation of intracellular signal transduction. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_145041.4

Inheritance

—

ClinVar variants

U:35B:5

Top phenotype

Neuromuscular disease

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr17:43,211,835-43,220,041

External References & Databases

Ensembl (ENSG00000184988)

Transcript & Mutation Effects

hg38 • Region Span ~8.2 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 TMEM106A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 2

Neuromuscular diseaseTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145041.4. 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			35 clinvar	3 clinvar	1 clinvar	39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	3	2	40

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145041.4	RefSeq	NP_659478.1	7	MANE Select
ENST00000612339.4	Ensembl	ENSP00000483246.1	7	MANE Select
NM_001291586.2	RefSeq	NP_001278515.1	7	Standard
NM_001291587.2	RefSeq	NP_001278516.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TYROBP Causal Network

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000331615
Coding exons: 7
Length: 8208
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125747
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.583	125	145	0.864	0.00000794	1700
Missense (PolyPhen)		45	48.38	0.93014		619
Synonymous	1.83	43	61.2	0.703	0.00000347	536
Loss of Function	0.328	11	12.2	0.899	6.21e-7	138

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.834
RVIS EVS: 0.19
RVIS percentile EVS: 66.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.204

Gene Damage Prediction

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