TMEM42

TMEM42
Identifiers
AliasesTMEM42, transmembrane protein 42
External IDsMGI: 1277176; HomoloGene: 11917; GeneCards: TMEM42; OMA:TMEM42 - orthologs
Orthologs
SpeciesHumanMouse
Entrez

131616

66079

Ensembl

ENSG00000169964
ENSG00000280516

ENSMUSG00000066233

UniProt

Q69YG0

Q9CR22

RefSeq (mRNA)

NM_144638

NM_001164823
NM_025339

RefSeq (protein)

NP_653239

NP_001158295
NP_079615

Location (UCSC)Chr 3: 44.86 – 44.87 MbChr 9: 122.85 – 122.85 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Transmembrane protein 42 (TMEM42) is a protein which in humans is encoded by the TMEM42 gene.[5] TMEM42 and its associated proteins may play a role in development and maintenance of the retina.[6][7][8][9]

Gene

The TMEM42 gene is located on the plus strand of the short arm on human chromosome 3 at cytogenetic band 3p21.31.[5] The gene spans 3,752 base pairs. The gene contains 3 exons.[5]

Regulation

TMEM42 has a ubiquitous variable expression, with approximately a 5x range.[5] It is expressed across all human tissues.[10][5]

mRNA

TMEM42 only has one transcript variant.[5] This transcript is 977 nucleotides long.[11] The transcript has a short 5' UTR. It has one predicted polyadenylation signal and site location.[5]

Protein

There is only one TMEM42 isoform.[12] The TMEM42 protein is 159 amino acids long and has 4 transmembrane regions.[12]

It has a molecular weight of about 17 kDa and an isoelectric point of about 9 pI.[13] Based of its highest scoring predicted structure, the TMEM42 protein has four alpha helices.[14][15] Topological predictions point to the majority of the protein being on the inside of the cell, with only 7 amino acids being on the extracellular side.[16]

TMEM42 has two standard deviations lower amounts of aspartate compared to the average human protein.[17]

Regulation

Experimental evidence points TMEM42 subcellular localization to the nucleoplasm, whereas computational predictions point to the endoplasmic reticulum and Golgi apparatus.[18][19][20] Due to TMEM42 being largely intercellular, it has 26 predicted phosphorylation sites.[21]

Homology and evolution

Paralogs

There are no known human paralogs of this gene. There is an animal paralog, TMEM42a, estimated to appear 429 million years ago in zebrafish.[22]

Orthologs

As seen in the table below, TMEM42 first appeared in fungi 1.27 billion years ago. This following table represents small selection of TMEM42 orthologs, identified via NCBI BLAST.[23] Across 20 orthologs in the table below, seven amino acids are conserved across all 20 organisms.

Genus and species Common name Taxonomic group Median date of divergence from humans (mya) Accession number Sequence length (aa) Sequence identity (%) to human protein[24] Sequence similarity (%) to human protein[24]
Homo sapiens Human Primates 0 NP_653239.1 159 100 100
Pan troglodytes Chimpanzee Primates 6 NP_001229549.3 159 99.4 99.4
Manis pentadactyla Chinese pangolin Pholidota 94 XP_036739795.2 159 81.1 84.3
Euleptes europaea Tarantolino Squamata 319 XP_056713860.1 147 33.9 45.7
Heteronotia binoei Prickly gecko Squamata 319 XP_060104087.1 147 32.3 42.5
Carettochelys insculpta Pitted-shelled turtle Testudines 319 XP_074842191.1 149 32.1 43.7
Calidris pugnax Ruff Charadriiformes 319 XP_014813517.1 152 34.3 47.4
Dromaius novaehollandiae Emu Casuariiformes 319 XP_064362502.1 135 31.0 43.7
Manacus vitellinus Golden-collared manakin Passeriformes 319 XP_029817613.1 175 26.2 35.7
Rhinatrema bivittatum Two-lined caecilian Gymnophiona 352 XP_029445552.1 178 33.2 51.1
Spea bombifrons Plains spadefoot toad Anura 352 XP_053324228.1 144 31.3 44.5
Pleurodeles waltl Iberian ribbed newt Urodela 352 XP_069067612.1 158 31.9 44.5
Lates calcarifer Barramundi perch Carangiformes 429 XP_018536264.1 150 29.8 42.0
Coregonus clupeaformis Lake whitefish Salmoniformes 429 XP_041707945.1 127 29.4 41.2
Electrophorus electricus Electric eel Gymnotiformes 429 XP_026886815.1 155 27.7 40.0
Zootermopsis nevadensis Nevada termite Blattodea 686 XP_021923555.1 125 29.8 41.7
Anabrus simplex Mormon cricket Orthoptera 686 XP_067001956.2 129 25.0 38.1
Aedes albopictus Asian tiger mosquito Diptera 686 XP_029713444.1 135 21.1 36.7
Coemansia javaensis N/A Zoopagomycotan 1275 KAJ2786225.1 127 28.2 37.1
Coemansia spiralis N/A Zoopagomycotan 1275 KAJ2708432.1 153 22.0 32.4

Interacting proteins

Notable protein interactions of human TMEM42[7]
Protein Name Extended Name Description
TLCD5 TLC Domain Containing 5 Role in human retina and lipid metabolism[8]
CCDC24 Coiled-Coil Domain Containing 24 Retinal development[9]
WFDC5 WAP Four-Disulfide Core Domain 5 Protease inhibitor[25]
UBE2I SUMO-conjugating enzyme UBC9 Performs conjugation step of sumoylation process
KIF15 Kinesin family member 15 Maintains spindle apparatus during mitosis[26]

Clinical significance

TMEM42 contains two cis-eQTLs, one on the promoter sequence and one on the 5' UTR.[27] TMEM42 has been implicated as a protective factor against papillary renal cell carcinoma.[6]

RNA-binding protein MBNL1 has 8 predicted binding sites on the TMEM42 transcript.[28] Impairments in MBNL1 function are associated with myotonic dystrophy.[29] Vastus lateralis biopises showed significantly reduced TMEM42 abundance in those with myotonic dystrophy type 2.[30]

References

  1. ^ a b c ENSG00000280516 GRCh38: Ensembl release 89: ENSG00000169964, ENSG00000280516 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000066233 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ a b c d e f g "TMEM42 transmembrane protein 42 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2025-12-04.
  6. ^ a b Wang, Yutao; Yan, Kexin; Lin, Jiaxing; Wang, Jianfeng; Zheng, Zhenhua; Li, Xinxin; Hua, Zhixiong; Bu, Yuepeng; Shi, Jianxiu; Sun, Siqing; Li, Xuejie; Liu, Yang; Bi, Jianbin (2020-11-05). "Three-gene risk model in papillary renal cell carcinoma: a robust likelihood-based survival analysis". Aging. 12 (21): 21854–21873. doi:10.18632/aging.104001. ISSN 1945-4589. PMC 7695399. PMID 33154194.
  7. ^ a b "STRING: functional protein association networks". string-db.org. Retrieved 2025-12-04.
  8. ^ a b Lim, Austin; Gunawan, Merry; Barathi, Veluchamy (June 2025). "Tlcd5 regulates ceramide metabolism and may be a neuroprotective mechanism in the retina". Investigative Ophthalmology & Visual Science. 66 (8) – via IOVS.
  9. ^ a b "Gene - CCDC24". maayanlab.cloud. Retrieved 2025-12-12.
  10. ^ "GDS3113 / 199615". www.ncbi.nlm.nih.gov. Retrieved 2025-12-12.
  11. ^ "Homo sapiens transmembrane protein 42 (TMEM42), mRNA". NCBI Nucleotide. 27 April 2025.
  12. ^ a b "transmembrane protein 42 [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2025-12-04.
  13. ^ "Expasy - Compute pI/Mw tool". web.expasy.org. Retrieved 2025-12-04.
  14. ^ "I-TASSER server for protein structure and function prediction". aideepmed.com. Retrieved 2025-12-12.
  15. ^ "AlphaFold Protein Structure Database". alphafold.ebi.ac.uk. Retrieved 2025-12-12.
  16. ^ "Protter - interactive protein feature visualization". wlab.ethz.ch. Archived from the original on 2025-08-27. Retrieved 2025-12-12.
  17. ^ EMBL-EBI; Institute, European Bioinformatics. "Job Dispatcher homepage | EMBL-EBI". www.ebi.ac.uk. Retrieved 2025-12-12.
  18. ^ "Subcellular - TMEM42 - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2025-12-04.
  19. ^ "PSORT II Prediction". psort.hgc.jp. Retrieved 2025-12-12.
  20. ^ "DeepLoc 2.1 - DTU Health Tech - Bioinformatic Services". services.healthtech.dtu.dk. Retrieved 2025-12-12.
  21. ^ "NetPhos 3.1 - DTU Health Tech - Bioinformatic Services". services.healthtech.dtu.dk. Retrieved 2025-12-12.
  22. ^ "tmem42a transmembrane protein 42a [Danio rerio (zebrafish)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2025-12-04.
  23. ^ "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2025-12-12.
  24. ^ a b EMBL-EBI; Institute, European Bioinformatics. "Job Dispatcher homepage | EMBL-EBI". www.ebi.ac.uk. Retrieved 2025-12-04.
  25. ^ "UniProt". UniProt. Retrieved 2025-12-12.
  26. ^ "KIF15 kinesin family member 15 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2025-12-12.
  27. ^ "FIVEx: eQTL Browser". fivex.sph.umich.edu. Retrieved 2025-12-04.
  28. ^ "RBPDB: The database of RNA-binding specificities". rbpdb.ccbr.utoronto.ca. Retrieved 2025-12-12.
  29. ^ Ho, Thai H.; Charlet-B, Nicolas; Poulos, Michael G.; Singh, Gopal; Swanson, Maurice S.; Cooper, Thomas A. (2004-08-01). "Muscleblind proteins regulate alternative splicing". The EMBO Journal. 23 (15): 3103–3112. doi:10.1038/sj.emboj.7600300. ISSN 1460-2075. PMC 514918. PMID 15257297.
  30. ^ "TMEM42 - GEO Profiles - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2025-12-12.
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