TMEM147

gene
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Also known as NIFIE14MGC1936

Summary

TMEM147 (transmembrane protein 147, HGNC:30414) is a protein-coding gene on chromosome 19q13.12, encoding BOS complex subunit TMEM147 (Q9BVK8). Component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes.

Enables ribosome binding activity. Involved in multi-pass transmembrane protein insertion into ER membrane and protein localization to nuclear inner membrane. Located in nuclear membrane. Part of multi-pass translocon complex. Is active in endoplasmic reticulum membrane.

Source: NCBI Gene 10430 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): neurodevelopmental disorder with facial dysmorphism, absent language, and pseudo-pelger-huet anomaly (Strong, GenCC) — +1 more curated relationship
  • GWAS associations: 2
  • Clinical variants (ClinVar): 67 total — 10 pathogenic, 1 likely-pathogenic
  • Phenotypes (HPO): 44
  • MANE Select transcript: NM_032635

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30414
Approved symbolTMEM147
Nametransmembrane protein 147
Location19q13.12
Locus typegene with protein product
StatusApproved
AliasesNIFIE14, MGC1936
Ensembl geneENSG00000105677
Ensembl biotypeprotein_coding
OMIM613585
Entrez10430

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 10 protein_coding, 5 retained_intron, 1 nonsense_mediated_decay

ENST00000222284, ENST00000392204, ENST00000392205, ENST00000477168, ENST00000593027, ENST00000595180, ENST00000595467, ENST00000596232, ENST00000599895, ENST00000909147, ENST00000909148, ENST00000909149, ENST00000928928, ENST00000928929, ENST00000928930, ENST00000928931

RefSeq mRNA: 3 — MANE Select: NM_032635 NM_001242597, NM_001242598, NM_032635

CCDS: CCDS12466, CCDS56091

Canonical transcript exons

ENST00000222284 — 7 exons

ExonStartEnd
ENSE000007000653554694535547029
ENSE000007000663554667235546808
ENSE000031059793554562635545816
ENSE000036207913554711935547240
ENSE000036510273554732435547526
ENSE000036692393554588835545957
ENSE000037549923554652635546585

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 98.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 63.9178 / max 340.2157, expressed in 1822 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
17534660.65231822
1753471.66151065
1753451.2514760
1753480.3526136

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right adrenal glandUBERON:000123398.44gold quality
left adrenal glandUBERON:000123498.34gold quality
right adrenal gland cortexUBERON:003582798.25gold quality
stromal cell of endometriumCL:000225598.24gold quality
left adrenal gland cortexUBERON:003582598.24gold quality
apex of heartUBERON:000209898.01gold quality
adrenal cortexUBERON:000123597.99gold quality
lower esophagus mucosaUBERON:003583497.91gold quality
body of pancreasUBERON:000115097.88gold quality
skin of legUBERON:000151197.76gold quality
right lobe of thyroid glandUBERON:000111997.73gold quality
left lobe of thyroid glandUBERON:000112097.62gold quality
skin of abdomenUBERON:000141697.58gold quality
adrenal glandUBERON:000236997.47gold quality
zone of skinUBERON:000001497.16gold quality
mucosa of transverse colonUBERON:000499197.13gold quality
left coronary arteryUBERON:000162697.12gold quality
thyroid glandUBERON:000204697.08gold quality
right atrium auricular regionUBERON:000663197.04gold quality
body of stomachUBERON:000116197.02gold quality
islet of LangerhansUBERON:000000696.99gold quality
gastrocnemiusUBERON:000138896.99gold quality
adenohypophysisUBERON:000219696.97gold quality
heart left ventricleUBERON:000208496.96gold quality
pancreasUBERON:000126496.88gold quality
ascending aortaUBERON:000149696.85gold quality
thoracic aortaUBERON:000151596.85gold quality
right coronary arteryUBERON:000162596.82gold quality
right testisUBERON:000453496.81gold quality
metanephros cortexUBERON:001053396.81gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-8271yes7.04
E-ANND-3no0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 5)

  • TMEM147 is a novel core component of the Nicalin-NOMO complex, further emphasizing its similarity with gamma-secretase. (PMID:20538592)
  • Regulation of ER Composition and Extent, and Putative Action in Protein Networks by ER/NE Protein TMEM147. (PMID:34638576)
  • Bi-allelic loss-of-function variants in TMEM147 cause moderate to profound intellectual disability with facial dysmorphism and pseudo-Pelger-Huet anomaly. (PMID:36044892)
  • TMEM147 Correlates with Immune Infiltration and Serve as a Potential Prognostic Biomarker in Hepatocellular Carcinoma. (PMID:37305689)
  • A biallelic loss-of-function variant in TMEM147 causes profound intellectual disability and spasticity. (PMID:37668766)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotmem147ENSDARG00000039913
mus_musculusTmem147ENSMUSG00000006315
rattus_norvegicusTmem147ENSRNOG00000021006
drosophila_melanogasterCG5861FBGN0015338
caenorhabditis_elegansWBGENE00022734

Protein

Protein identifiers

BOS complex subunit TMEM147Q9BVK8 (reviewed: Q9BVK8)

Alternative names: Protein NIFIE 14, Transmembrane protein 147

All UniProt accessions (3): Q9BVK8, A8MU21, K7ELX3

UniProt curated annotations — full annotation on UniProt →

Function. Component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes. The MPT complex takes over after the SEC61 complex: following membrane insertion of the first few transmembrane segments of proteins by the SEC61 complex, the MPT complex occludes the lateral gate of the SEC61 complex to promote insertion of subsequent transmembrane regions. Also acts as a negative regulator of CHRM3 function, most likely by interfering with its trafficking to the cell membrane. Negatively regulates CHRM3-mediated calcium mobilization and activation of RPS6KA1/p90RSK activity. Regulates LBR localization to the nucleus inner membrane.

Subunit / interactions. Component of the back of Sec61 (BOS) complex, composed of NCLN/Nicalin, NOMO (NOMO1, NOMO2 or NOMO3) and TMEM147. The BOS complex is part of the multi-pass translocon (MPT) complex, composed of three subcomplexes, the GEL complex (composed of RAB5IF/OPTI and TMCO1), the BOS complex (composed of NCLN/Nicalin, NOMO and TMEM147) and the PAT complex (composed of WDR83OS/Asterix and CCDC47). The MPT complex associates with the SEC61 complex. Interacts with CHRM3, CHRM1 and AVPR2. Interacts with LBR; promoting LBR localization to the nucleus inner membrane. Interacts with DHCR7.

Subcellular location. Endoplasmic reticulum membrane. Nucleus membrane. Cell membrane.

Disease relevance. Neurodevelopmental disorder with facial dysmorphism, absent language, and pseudo-Pelger-Huet anomaly (NEDFLPH) [MIM:620075] An autosomal recessive disorder with onset in infancy and characterized by global developmental delay, intellectual disability, dysmorphic facial features, coarse facies, and behavioral problems. Affected individuals may have variable findings on brain imaging, such as cortical atrophy, thin corpus callosum and enlarged ventricles. Laboratory studies show nuclear lobulation defects in a subset of neutrophils, indicating a pseudo-Pelger-Huet anomaly. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the TMEM147 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BVK8-11yes
Q9BVK8-22

RefSeq proteins (3): NP_001229526, NP_001229527, NP_116024* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019164TMEM147Family

Pfam: PF09767

UniProt features (28 total): transmembrane region 7, topological domain 7, sequence variant 7, sequence conflict 5, chain 1, splice variant 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
9C7UELECTRON MICROSCOPY3.65
6W6LELECTRON MICROSCOPY3.84
9C7VELECTRON MICROSCOPY6.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BVK8-F192.380.74

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 288 (showing top): FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN, KAAB_FAILED_HEART_ATRIUM_DN, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, CREB_Q4, MORF_ATOX1, ATF1_Q6, WTGAAAT_UNKNOWN, LUI_TARGETS_OF_PAX8_PPARG_FUSION, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE, MORF_PPP2R4, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, ATF3_Q6, MORF_GPX4, HFH1_01, FREAC4_01

GO Biological Process (2): protein localization to nuclear inner membrane (GO:0036228), multi-pass transmembrane protein insertion into ER membrane (GO:0160063)

GO Molecular Function (2): ribosome binding (GO:0043022), protein binding (GO:0005515)

GO Cellular Component (8): endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), nuclear membrane (GO:0031965), protein-containing complex (GO:0032991), multi-pass translocon complex (GO:0160064), nucleus (GO:0005634), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
organelle membrane2
intracellular membrane-bounded organelle2
protein localization to membrane1
protein localization to nuclear envelope1
protein insertion into ER membrane1
ribonucleoprotein complex binding1
binding1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
membrane1
cell periphery1
nucleus1
nuclear envelope1
cellular_component1
ER membrane insertion complex1
cytoplasm1
endomembrane system1
cellular anatomical structure1

Protein interactions and networks

STRING

1308 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TMEM147NCLNQ969V3991
TMEM147NOMO2Q5JPE7986
TMEM147NOMO3P69849718
TMEM147TMEM63AO94886651
TMEM147ERG28Q9UKR5624
TMEM147NOMO1P78421611
TMEM147YIPF6Q96EC8593
TMEM147EMC7Q9NPA0587
TMEM147GALMQ96C23578
TMEM147IER3IP1Q9Y5U9573
TMEM147TMEM53Q6P2H8556
TMEM147XYLT1Q86Y38549
TMEM147TMEM223A0PJW6540
TMEM147CCDC47Q96A33534
TMEM147KRTCAP2Q8N6L1477

IntAct

177 interactions, top by confidence:

ABTypeScore
LDLRAD1TMEM147psi-mi:“MI:0915”(physical association)0.780
CREB3L1TMEM147psi-mi:“MI:0915”(physical association)0.780
TMEM147LDLRAD1psi-mi:“MI:0915”(physical association)0.780
TMEM147CREB3L1psi-mi:“MI:0915”(physical association)0.780
TMEM147PACC1psi-mi:“MI:0915”(physical association)0.740
HTR2CTMEM147psi-mi:“MI:0915”(physical association)0.740
ABHD16ATMEM147psi-mi:“MI:0915”(physical association)0.670
TMEM147SYNE4psi-mi:“MI:0915”(physical association)0.560
SYNE4TMEM147psi-mi:“MI:0915”(physical association)0.560
TMEM147GPR37L1psi-mi:“MI:0915”(physical association)0.560
TMEM147CLRN1psi-mi:“MI:0915”(physical association)0.560
TMEM147SHISA3psi-mi:“MI:0915”(physical association)0.560
TMEM147SLC10A1psi-mi:“MI:0915”(physical association)0.560
TMEM147LHFPL2psi-mi:“MI:0915”(physical association)0.560
TMEM147PVRpsi-mi:“MI:0915”(physical association)0.560
TMEM147psi-mi:“MI:0915”(physical association)0.560
TMEM147TEX29psi-mi:“MI:0915”(physical association)0.560
TMEM147IL3RApsi-mi:“MI:0915”(physical association)0.560

BioGRID (104): CREB3L1 (Two-hybrid), SYNE4 (Two-hybrid), LDLRAD1 (Two-hybrid), TMEM147 (Two-hybrid), ABI3 (Two-hybrid), TMEM147 (Affinity Capture-MS), TMEM147 (Affinity Capture-MS), TMEM147 (Positive Genetic), TMEM147 (Two-hybrid), TMEM147 (Two-hybrid), TMEM147 (Two-hybrid), TMEM147 (Two-hybrid), TMEM147 (Two-hybrid), TMEM147 (Two-hybrid), TSPAN12 (Two-hybrid)

ESM2 similar proteins: A0A078H868, A0A8I3MKU8, A1C7T5, A1DIF7, A2R616, A6S950, B0XUW3, B2B2N5, B6HJA3, B8N6H2, B9RK42, C0NLX2, C0RZV6, C1G565, C1GZK1, C4JDF8, C5FZ62, C5GN10, C5JCV0, C5PEI5, C6H4B5, C7Z7C3, D1ZIW5, D4AT37, D4DGR3, I6VSD2, O94673, O96005, Q0CVD7, Q0IJ20, Q28FY5, Q29BL9, Q2H0U8, Q2TA63, Q2UDE5, Q3SZR6, Q4WZS1, Q5BBC6, Q5BIY5, Q6DFI2

Diamond homologs: A0A8I3MKU8, I6VSD2, Q28FY5, Q2TA63, Q3SZR6, Q6DFI2, Q6DGL7, Q9BVK8, Q9CQG6

SIGNOR signaling

3 interactions.

AEffectBMechanism
TMEM147“form complex”“BOS complex, NOMO1 variant”binding
TMEM147“form complex”“BOS complex, NOMO2 variant”binding
TMEM147“form complex”“BOS complex, NOMO3 variant”binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

67 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic10
Likely pathogenic1
Uncertain significance37
Likely benign4
Benign1

Top pathogenic / likely-pathogenic (11)

Variant IDHGVSClassification
1708019NM_032635.4(TMEM147):c.100_118del (p.Lys34fs)Pathogenic
1708020NM_032635.4(TMEM147):c.419dup (p.Asn140fs)Pathogenic
1708024NM_032635.4(TMEM147):c.345-1G>TPathogenic
1708025NM_032635.4(TMEM147):c.390G>A (p.Trp130Ter)Pathogenic
1708026NM_032635.4(TMEM147):c.540_543dup (p.Val182fs)Pathogenic
1708028NM_032635.4(TMEM147):c.486C>G (p.Tyr162Ter)Pathogenic
1711114NM_032635.4(TMEM147):c.169_172del (p.Phe57fs)Pathogenic
1712322NM_032635.4(TMEM147):c.163_172del (p.Thr55fs)Pathogenic
3602549NM_032635.4(TMEM147):c.429+2T>CPathogenic
3778700NM_032635.4(TMEM147):c.208-8_222delinsCTPathogenic
3374729NM_032635.4(TMEM147):c.430-2A>TLikely pathogenic

SpliceAI

642 predictions. Top by Δscore:

VariantEffectΔscore
19:35545812:GGCCT:Gdonor_gain1.0000
19:35545813:GCCT:Gdonor_gain1.0000
19:35545813:GCCTG:Gdonor_gain1.0000
19:35545817:G:GGdonor_gain1.0000
19:35545956:AGGT:Adonor_loss1.0000
19:35545959:T:Adonor_loss1.0000
19:35546670:A:AGacceptor_gain1.0000
19:35546670:AG:Aacceptor_gain1.0000
19:35546671:G:GGacceptor_gain1.0000
19:35546671:GG:Gacceptor_gain1.0000
19:35546671:GGA:Gacceptor_gain1.0000
19:35546749:A:Tdonor_gain1.0000
19:35546805:CCCGG:Cdonor_loss1.0000
19:35546807:CGG:Cdonor_loss1.0000
19:35546809:G:GAdonor_loss1.0000
19:35546809:G:GGdonor_gain1.0000
19:35547025:GTCTG:Gdonor_gain1.0000
19:35547227:GCC:Gdonor_gain1.0000
19:35547238:GGA:Gdonor_gain1.0000
19:35547239:GAG:Gdonor_gain1.0000
19:35547241:G:GGdonor_gain1.0000
19:35546583:GGG:Gdonor_gain0.9900
19:35546584:GG:Gdonor_gain0.9900
19:35546584:GGG:Gdonor_gain0.9900
19:35546585:GG:Gdonor_gain0.9900
19:35546585:GGTGA:Gdonor_loss0.9900
19:35546586:G:GAdonor_loss0.9900
19:35546587:T:Adonor_loss0.9900
19:35546671:GGAGT:Gacceptor_gain0.9900
19:35546747:G:GTdonor_gain0.9900

AlphaMissense

1466 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:35545925:G:AG39R1.000
19:35545925:G:CG39R1.000
19:35546777:G:CG105R1.000
19:35546780:T:AW106R1.000
19:35546780:T:CW106R1.000
19:35546782:G:CW106C1.000
19:35546782:G:TW106C1.000
19:35546958:T:AW120R1.000
19:35546958:T:CW120R1.000
19:35546982:T:CF128L1.000
19:35546983:T:CF128S1.000
19:35546983:T:GF128C1.000
19:35546984:T:AF128L1.000
19:35546984:T:GF128L1.000
19:35546988:T:AW130R1.000
19:35546988:T:CW130R1.000
19:35545759:G:AG7E0.999
19:35545763:C:AN8K0.999
19:35545763:C:GN8K0.999
19:35545764:T:CC9R0.999
19:35545765:G:AC9Y0.999
19:35545766:C:GC9W0.999
19:35545771:C:AA11D0.999
19:35545774:T:AL12H0.999
19:35545786:C:AP16H0.999
19:35545800:T:GY21D0.999
19:35545917:T:AV36D0.999
19:35545926:G:AG39E0.999
19:35545950:T:CL47P0.999
19:35545952:T:CC48R0.999

dbSNP variants (sampled 300 via entrez): RS1000513581 (19:35546017 G>A), RS1001088815 (19:35544644 C>T), RS1001207725 (19:35547327 C>A,T), RS1002625632 (19:35547908 G>C), RS1003549329 (19:35546066 C>T), RS1003653580 (19:35546700 C>G), RS1005633805 (19:35547079 C>G), RS1005727157 (19:35546790 C>T), RS1006746426 (19:35545442 C>T), RS1007107284 (19:35545363 C>T), RS1007615253 (19:35544424 G>A,C), RS1007858150 (19:35546408 A>G), RS1008108980 (19:35543642 G>A), RS1009845012 (19:35544442 T>G), RS1010161018 (19:35544575 T>C)

Disease associations

OMIM: gene MIM:613585 | disease phenotypes: MIM:620075

GenCC curated gene-disease

DiseaseClassificationInheritance
neurodevelopmental disorder with facial dysmorphism, absent language, and pseudo-pelger-huet anomalyStrongAutosomal recessive
complex neurodevelopmental disorderModerateAutosomal recessive

Mondo (2): neurodevelopmental disorder with facial dysmorphism, absent language, and pseudo-pelger-huet anomaly (MONDO:0859298), complex neurodevelopmental disorder (MONDO:0100038)

Orphanet (1): Global developmental delay-intellectual disability-facial dysmorphism-pseudo-Pelger-Huët anomaly syndrome (Orphanet:698085)

HPO phenotypes

44 total (30 of 44 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000154Wide mouth
HP:0000179Thick lower lip vermilion
HP:0000219Thin upper lip vermilion
HP:0000232Everted lower lip vermilion
HP:0000276Long face
HP:0000280Coarse facial features
HP:0000286Epicanthus
HP:0000316Hypertelorism
HP:0000319Smooth philtrum
HP:0000343Long philtrum
HP:0000369Low-set ears
HP:0000407Sensorineural hearing impairment
HP:0000494Downslanted palpebral fissures
HP:0000664Synophrys
HP:0000718Aggressive behavior
HP:0000739Anxiety
HP:0000750Delayed speech and language development
HP:0000752Hyperactivity
HP:0000954Single transverse palmar crease
HP:0001249Intellectual disability
HP:0001252Hypotonia
HP:0001270Motor delay
HP:0001335Bimanual synkinesia
HP:0001344Absent speech
HP:0001631Atrial septal defect
HP:0001655Patent foramen ovale
HP:0002188Delayed CNS myelination
HP:0002212Curly hair
HP:0002751Kyphoscoliosis

GWAS associations

2 associations (top):

StudyTraitp-value
GCST90011898_58Alanine aminotransferase levels6.000000e-12
GCST90013405_116Liver enzyme levels (alanine transaminase)2.000000e-16

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, increases methylation3
sodium arsenitedecreases expression2
bisphenol Aaffects expression1
beta-lapachonedecreases expression1
arseniteaffects binding, increases reaction1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
Diazinonincreases methylation1
Diurondecreases expression1
Doxorubicinincreases expression1
Ethyl Methanesulfonatedecreases expression1
Hydrogen Peroxideaffects expression1
Methyl Methanesulfonatedecreases expression1
Smokedecreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases expression1
Cyclosporineincreases expression1
Aflatoxin B1increases methylation1
Copper Sulfatedecreases expression1
Lactic Aciddecreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B3JIAbcam HEK293T TMEM147 KOTransformed cell lineFemale

Clinical trials (associated diseases)

2 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT06310681Not specifiedCOMPLETEDPilot Testing of a Co-adapted Group Programme for Parents/Carers of Children With Complex Neurodisability
NCT07303049Not specifiedNOT_YET_RECRUITINGCognitive Benefit of Intensive Rehabilitation Using Rhythmic Music Training in Children With Complex Neurodevelopmental Disorder