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GeneE
8 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
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TMEM53
transmembrane protein 53
Chromosome 1 Β· 1p34.1
NCBI Gene: 79639Ensembl: ENSG00000126106.14HGNC: HGNC:26186UniProt: Q5TDE2
13PubMed Papers
21Diseases
0Drugs
2Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
negative regulation of ossificationnegative regulation of BMP signaling pathwayregulation of nucleocytoplasmic transportnucleuscraniotubular dysplasia, Ikegawa typeleukodystrophy, hypomyelinating, 23, with ataxia, deafness, liver dysfunction, and dilated cardiomyopathybrachydactylous dwarfism, Mseleni typeX-linked non-syndromic intellectual disability
✦AI Summary

TMEM53 is a nuclear envelope transmembrane protein with dual roles in bone homeostasis and viral restriction. Functionally, TMEM53 negatively regulates bone morphogenetic protein (BMP) signaling by blocking the cytoplasm-nucleus translocation of phosphorylated SMAD1/5/9 proteins in osteoblast lineage cells, thereby suppressing osteogenesis 1. This regulatory mechanism involves TMEM53's transmembrane domain, which is essential for its molecular interactions 2. Beyond skeletal biology, TMEM53 functions as a novel intrinsic antiviral factor against swine acute diarrhea syndrome coronavirus (SADS-CoV), where it interacts with viral non-structural protein 12 to disrupt RNA-dependent RNA polymerase assembly and viral replication independently of interferon signaling 2. Biallelic loss-of-function TMEM53 variants cause craniotubular dysplasia, Ikegawa type (CTDI), an autosomal recessive sclerosing bone disorder characterized by dysregulated BMP-SMAD signaling and accelerated bone formation 1. Clinical manifestations include calvarial thickening, skeletal modeling abnormalities, and notably, progressive childhood blindness due to optic canal narrowing 34. Pathogenic variants include nonsense mutations, deletions affecting splice sites, and novel missense mutations that introduce ubiquitination sites triggering protein degradation 5. TMEM53 also regulates cell cycle progression through p53-dependent pathways, influencing stress-induced senescence 6.

Sources cited
1
TMEM53 negatively regulates BMP signaling by blocking SMAD protein nuclear translocation in osteoblasts; biallelic loss-of-function variants cause sclerosing bone disorder and craniotubular dysplasia, Ikegawa type
PMID: 33824347
2
TMEM53 acts as a SADS-CoV restriction factor by interacting with viral NSP12 and disrupting RNA-dependent RNA polymerase assembly independently of interferon responses; transmembrane domain is essential for antiviral activity
PMID: 37584551
3
TMEM53 deficiency causes craniotubular dysplasia with skeletal hyperostosis and progressive childhood blindness due to optic canal narrowing; clinical features include accelerated bone formation and high bone turnover
PMID: 39084544
4
Novel TMEM53 missense variants identified in craniotubular dysplasia patients with progressive visual loss; optic canal decompression surgery demonstrated clinical improvement
PMID: 39901041
5
A missense variant (p.E212K) introduces a novel ubiquitination site causing TMEM53 protein degradation via the ubiquitin-proteasome system, causing disease through altered post-translational modification
PMID: 40680154
6
TMEM53 regulates stress-dependent cell cycle withdrawal through p53-dependent pathways, affecting retinoblastoma protein phosphorylation and promoting cellular senescence
PMID: 21533191
Disease Associationsβ“˜21
craniotubular dysplasia, Ikegawa typeOpen Targets
0.50Moderate
leukodystrophy, hypomyelinating, 23, with ataxia, deafness, liver dysfunction, and dilated cardiomyopathyOpen Targets
0.45Moderate
brachydactylous dwarfism, Mseleni typeOpen Targets
0.10Suggestive
Bartter syndromeOpen Targets
0.09Suggestive
SHOX-related short statureOpen Targets
0.09Suggestive
X-linked non-syndromic intellectual disabilityOpen Targets
0.09Suggestive
chromosome 22q11.2 deletion syndrome, distalOpen Targets
0.07Suggestive
Hyaluronidase deficiencyOpen Targets
0.06Suggestive
short stature due to partial GHR deficiencyOpen Targets
0.06Suggestive
Seckel syndrome 6Open Targets
0.06Suggestive
autosomal recessive primary microcephalyOpen Targets
0.06Suggestive
Bruck syndromeOpen Targets
0.05Suggestive
spondyloepimetaphyseal dysplasia with multiple dislocationsOpen Targets
0.05Suggestive
brachyolmia, Maroteaux typeOpen Targets
0.05Suggestive
spondyloperipheral dysplasiaOpen Targets
0.05Suggestive
Spondyloperipheral dysplasia - short ulnaOpen Targets
0.05Suggestive
spondylometaphyseal dysplasia, A4 typeOpen Targets
0.05Suggestive
multiple epiphyseal dysplasia type 4Open Targets
0.05Suggestive
Cole-Carpenter syndromeOpen Targets
0.05Suggestive
progressive spondyloepimetaphyseal dysplasia-short stature-short fourth metatarsals-intellectual disability syndromeOpen Targets
0.05Suggestive
Craniotubular dysplasia, Ikegawa typeUniProt
Pathogenic Variants2
NM_024587.4(TMEM53):c.62-5_62-3delPathogenic
TMEM53-related craniotubular dysplasia|Craniotubular dysplasia, Ikegawa type
β˜…β˜…β˜†β˜†2020
NM_024587.4(TMEM53):c.219_222dup (p.Val75fs)Pathogenic
TMEM53-related craniotubular dysplasia|Craniotubular dysplasia, Ikegawa type
β˜…β˜†β˜†β˜†2020β†’ Residue 75
View on ClinVar β†—
Related Genes
CRIM1Shared pathway33%VWC2LShared pathway25%SKOR1Shared pathway25%SKOR2Shared pathway20%TRIM33Shared pathway20%SOSTShared pathway20%
Tissue Expression6 tissues
Liver
100%
Ovary
21%
Heart
20%
Lung
18%
Brain
17%
Bone Marrow
14%
Gene Interaction Network
Click a node to explore
TMEM53CRIM1VWC2LSKOR1SKOR2TRIM33SOST
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q5TDE2
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.98LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.63 [0.41–0.98]
RankingsWhere TMEM53 stands among ~20K protein-coding genes
  • #16,341of 20,598
    Most Researched13
  • #4,581of 5,498
    Most Pathogenic Variants2
  • #9,314of 17,882
    Most Constrained (LOEUF)0.98
Genes detectedTMEM53
Sources retrieved8 papers
Response timeβ€”
πŸ“„ Sources
8β–Ό
1
Identification of TMEM53 as a novel SADS-CoV restriction factor that targets viral RNA-dependent RNA polymerase.
PMID: 37584551
Emerg Microbes Infect Β· 2023
1.00
2
Deficiency of TMEM53 causes a previously unknown sclerosing bone disorder by dysregulation of BMP-SMAD signaling.
PMID: 33824347
Nat Commun Β· 2021
0.88
3
Novel TMEM53 missense variant generated a new ubiquitination site and cause Craniotubular dysplasia, Ikegawa type.
PMID: 40680154
Hum Mol Genet Β· 2025
0.75
4
Transmembrane protein 53 craniotubular dysplasia (OMIM # 619727): The skeletal disease and consequent blindness of this new disorder.
PMID: 39084544
Bone Β· 2024
0.63
5
Craniotubular Dysplasia Ikegawa Type: Further Delineation of the Phenotype.
PMID: 39300972
Am J Med Genet A Β· 2025
0.50