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SPEM2

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Summary

SPEM2 (SPEM family member 2, HGNC:27315) is a protein-coding gene on chromosome 17p13.1, encoding Uncharacterized protein SPEM2 (Q0P670).

Predicted to be located in membrane.

Source: NCBI Gene 201243 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 10 total — 1 pathogenic
  • MANE Select transcript: NM_175734

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:27315
Approved symbolSPEM2
NameSPEM family member 2
Location17p13.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000184560
Ensembl biotypeprotein_coding
Entrez201243

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000333870, ENST00000574034

RefSeq mRNA: 1 — MANE Select: NM_175734 NM_175734

CCDS: CCDS42255

Canonical transcript exons

ENST00000333870 — 3 exons

ExonStartEnd
ENSE0000129599974259937426050
ENSE0000129998674261887427568
ENSE0000132347274256167425826

Expression profiles

Bgee: expression breadth broad, 23 present calls, max score 96.04.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1033 / max 82.9996, expressed in 4 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1591860.06854
1591850.02643
1591870.00512
1591840.00332

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453396.04gold quality
right testisUBERON:000453496.04gold quality
testisUBERON:000047395.30gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.54gold quality
stromal cell of endometriumCL:000225539.60gold quality
skeletal muscle tissueUBERON:000113439.42gold quality
right coronary arteryUBERON:000162539.20silver quality
gastrocnemiusUBERON:000138839.05gold quality
muscle of legUBERON:000138338.05gold quality
metanephros cortexUBERON:001053337.32silver quality
colonic epitheliumUBERON:000039737.20gold quality
muscle tissueUBERON:000238536.67gold quality
right hemisphere of cerebellumUBERON:001489036.58gold quality
cortical plateUBERON:000534336.47gold quality
granulocyteCL:000009436.22gold quality
bone marrow cellCL:000209236.16gold quality
mucosa of transverse colonUBERON:000499136.11gold quality
hindlimb stylopod muscleUBERON:000425235.58gold quality
amygdalaUBERON:000187634.42silver quality
temporal lobeUBERON:000187134.38silver quality
Ammon’s hornUBERON:000195433.46gold quality
prefrontal cortexUBERON:000045133.23gold quality
descending thoracic aortaUBERON:000234532.32gold quality
multicellular organismUBERON:000046831.95gold quality
caudate nucleusUBERON:000187331.78gold quality
bone marrowUBERON:000237131.74gold quality
body of pancreasUBERON:000115031.57gold quality
right uterine tubeUBERON:000130231.27gold quality
tonsilUBERON:000237230.35gold quality
pancreasUBERON:000126430.33gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.16

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusSpem2ENSMUSG00000044084
rattus_norvegicusSpem2ENSRNOG00000058939

Protein

Protein identifiers

Uncharacterized protein SPEM2 — Q0P670 (reviewed: Q0P670)

All UniProt accessions (2): Q0P670, I3L1F6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_783861* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR031368SPEM1_NDomain

Pfam: PF15670

UniProt features (8 total): region of interest 2, sequence variant 2, chain 1, transmembrane region 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q0P670-F149.840.07

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 9 (showing top): AGGTGCA_MIR500, MARTENS_TRETINOIN_RESPONSE_UP, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_1H_UP, GSE9960_HEALTHY_VS_SEPSIS_PBMC_UP, GSE25088_CTRL_VS_IL4_STIM_STAT6_KO_MACROPHAGE_UP, GSE16385_UNTREATED_VS_12H_ROSIGLITAZONE_TREATED_MACROPHAGE_UP, HNF4_Q6, chr17p13

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure1

Protein interactions and networks

STRING

390 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SPEM2C17orf50Q8WW18668
SPEM2SPEM3A0A1B0GUW6625
SPEM2TLDC2A0PJX2602
SPEM2SPMAP1A8MV24581
SPEM2CFAP97D1B2RV13580
SPEM2CIMAP2Q3ZCV2510
SPEM2TSSK6Q9BXA6450
SPEM2TBC1D3KA0A087X1G2419
SPEM2KRTAP9-7A8MTY7419
SPEM2ODF2Q5BJF6410
SPEM2TLCD3AQ8TBR7398
SPEM2CDRT15L2A8MXV6396
SPEM2KIF21BO75037387
SPEM2OXCT2Q9BYC2378
SPEM2HTRA4P83105361

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GTH6, A0A1D5RMD1, A1KXM5, A2AEY4, A6NCI8, A6QQS3, A7KBS4, C4P6S0, O94713, P0C9Z7, P53963, P53976, Q0P670, Q0VAV2, Q10668, Q196W1, Q2KHR3, Q2YDJ5, Q32MG2, Q3V0A6, Q3V3Q4, Q4V8E9, Q5JRM2, Q68FV4, Q6AXV6, Q6AYN3, Q6NS59, Q7TSG5, Q80VJ6, Q80Y39, Q80YD3, Q810T2, Q86XD8, Q8C5U4, Q8CH19, Q8IWI9, Q8K4E0, Q8NDH2, Q8NEV8, Q8NFU7

Diamond homologs: Q0P670, Q32LJ5, Q5F289, Q68FV4, Q8C5U4, Q8N4L4, A0A1B0GUW6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance8
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
3243103NC_000017.10:g.(?7123304)(7360042_?)delPathogenic

SpliceAI

253 predictions. Top by Δscore:

VariantEffectΔscore
17:7426046:GAAAA:Gdonor_gain0.9900
17:7426051:G:GGdonor_gain0.9900
17:7426183:CCCA:Cacceptor_loss0.9800
17:7426184:CCA:Cacceptor_loss0.9800
17:7426186:A:AGacceptor_gain0.9800
17:7426186:A:Cacceptor_loss0.9800
17:7426186:AGAT:Aacceptor_gain0.9800
17:7426187:G:GGacceptor_gain0.9800
17:7426187:GAT:Gacceptor_gain0.9800
17:7426187:GATG:Gacceptor_gain0.9800
17:7426187:GATGA:Gacceptor_gain0.9700
17:7425823:TATGG:Tdonor_loss0.9600
17:7425826:GGT:Gdonor_loss0.9600
17:7425827:G:GGdonor_gain0.9600
17:7425827:G:Tdonor_loss0.9600
17:7425828:T:Gdonor_loss0.9600
17:7425829:C:CCdonor_loss0.9600
17:7425830:AG:Adonor_loss0.9600
17:7425831:G:Cdonor_loss0.9600
17:7425992:GAT:Gacceptor_gain0.9600
17:7426049:AA:Adonor_gain0.9600
17:7426050:AG:Adonor_loss0.9600
17:7426051:GTAAG:Gdonor_loss0.9600
17:7426052:T:TCdonor_loss0.9600
17:7426053:AAGT:Adonor_loss0.9600
17:7426187:GA:Gacceptor_gain0.9500
17:7425988:CCCA:Cacceptor_loss0.9400
17:7425990:CA:Cacceptor_loss0.9400
17:7425991:A:AGacceptor_gain0.9400
17:7425992:G:GGacceptor_gain0.9400

AlphaMissense

3261 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:7427378:A:CS463R0.959
17:7427380:C:AS463R0.959
17:7427380:C:GS463R0.959
17:7427324:T:CF445L0.950
17:7427326:T:AF445L0.950
17:7427326:T:GF445L0.950
17:7427392:G:CK467N0.915
17:7427392:G:TK467N0.915
17:7426673:A:CS228R0.910
17:7426675:T:AS228R0.910
17:7426675:T:GS228R0.910
17:7426256:T:CC89R0.903
17:7426251:T:CI87T0.901
17:7425802:C:AN38K0.897
17:7425802:C:GN38K0.897
17:7425782:G:CG32R0.890
17:7426258:C:GC89W0.884
17:7426251:T:GI87S0.881
17:7426463:T:CF158L0.880
17:7426465:C:AF158L0.880
17:7426465:C:GF158L0.880
17:7425996:T:AW48R0.879
17:7425996:T:CW48R0.879
17:7425792:T:AV35D0.875
17:7425806:G:CG40R0.868
17:7426251:T:AI87N0.866
17:7427376:A:TD462V0.856
17:7425814:C:AN42K0.855
17:7425814:C:GN42K0.855
17:7426743:C:TS251F0.851

dbSNP variants (sampled 300 via entrez): RS1001511596 (17:7425541 T>G), RS1001942494 (17:7425305 A>G), RS1002372128 (17:7424422 A>C), RS1002545419 (17:7424038 C>T), RS1003361594 (17:7427783 C>T), RS1003783812 (17:7425474 A>C,G), RS1004370704 (17:7428033 G>A), RS1006200879 (17:7423743 C>A), RS1007178821 (17:7425142 T>C,G), RS1007209826 (17:7424930 C>A), RS1007330050 (17:7426240 G>A,C), RS1007922699 (17:7427183 C>T), RS1009161442 (17:7426162 A>C), RS1009567488 (17:7427588 G>A), RS1009760338 (17:7424690 C>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:201475

GenCC curated gene-disease

Mondo (1): very long chain acyl-CoA dehydrogenase deficiency (MONDO:0008723)

Orphanet (1): Very long chain acyl-CoA dehydrogenase deficiency (Orphanet:26793)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST010043_31Asthma2.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
bisphenol Aaffects cotreatment, decreases expression1
Benzo(a)pyreneaffects methylation1
Dexamethasoneaffects cotreatment, decreases expression1
Indomethacinaffects cotreatment, decreases expression1
Valproic Acidincreases methylation1
1-Methyl-3-isobutylxanthineaffects cotreatment, decreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00983788PHASE2COMPLETEDEffect of Bezafibrate on Muscle Metabolism in Patients With Fatty Acid Oxidation Defects
NCT01886378PHASE2COMPLETEDA Study of UX007 (Triheptanoin) in Participants With Long-Chain Fatty Acid Oxidation Disorders (LC-FAOD)
NCT02214160PHASE2COMPLETEDLong-Chain Fatty Acid Oxidation Disorders (LC-FAOD) Extension Study for Subjects Previously Enrolled in Triheptanoin Studies
NCT01494051PHASE1/PHASE2COMPLETEDHigh Protein Diet in Patients With Long-chain Fatty Acid Oxidation Disorders
NCT05411835EARLY_PHASE1COMPLETEDOral Ketones and Exercise Among Patients With Long-chain Fatty Acid Oxidation Disorders
NCT02517307Not specifiedCOMPLETEDFatty Acid Oxidation Defects and Insulin Sensitivity
NCT02635269Not specifiedUNKNOWNFat and Sugar Metabolism During Exercise in Patients With Metabolic Myopathy
NCT03531554Not specifiedCOMPLETEDAcute Nutritional Ketosis in VLCAD Deficiency
NCT03655223Not specifiedENROLLING_BY_INVITATIONEarly Check: Expanded Screening in Newborns
NCT05910151Not specifiedUNKNOWNSelective Screening of Children for Hereditary Metabolic Diseases by Tandem Mass Spectrometry in Kazakhstan

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot