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SAPCD1

gene
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Also known as NG23

Summary

SAPCD1 (suppressor APC domain containing 1, HGNC:13938) is a protein-coding gene on chromosome 6p21.33, encoding Suppressor APC domain-containing protein 1 (Q5SSQ6).

At a glance

  • GWAS associations: 27
  • MANE Select transcript: NM_001039651

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13938
Approved symbolSAPCD1
Namesuppressor APC domain containing 1
Location6p21.33
Locus typegene with protein product
StatusApproved
AliasesNG23
Ensembl geneENSG00000228727
Ensembl biotypeprotein_coding
Entrez401251

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000415669, ENST00000425424, ENST00000494299, ENST00000927045

RefSeq mRNA: 1 — MANE Select: NM_001039651 NM_001039651

CCDS: CCDS34411

Canonical transcript exons

ENST00000415669 — 5 exons

ExonStartEnd
ENSE000035852383176426631764355
ENSE000037780003176341531763555
ENSE000037901153176406431764159
ENSE000039781893176443631764850
ENSE000039781903176265631763168

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 90.31.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0512 / max 20.3556, expressed in 17 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
670420.051217

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
skin of legUBERON:000151190.31gold quality
right uterine tubeUBERON:000130289.88gold quality
zone of skinUBERON:000001488.05gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.19gold quality
skin of abdomenUBERON:000141685.17gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.61gold quality
lower esophagus mucosaUBERON:003583482.81gold quality
metanephros cortexUBERON:001053382.72gold quality
mucosa of transverse colonUBERON:000499182.41gold quality
spleenUBERON:000210681.64gold quality
granulocyteCL:000009480.94gold quality
cortex of kidneyUBERON:000122580.84gold quality
pituitary glandUBERON:000000780.43gold quality
right testisUBERON:000453480.12gold quality
adenohypophysisUBERON:000219679.80gold quality
olfactory segment of nasal mucosaUBERON:000538679.54gold quality
ventricular zoneUBERON:000305379.12gold quality
tibial nerveUBERON:000132378.91gold quality
transverse colonUBERON:000115778.81gold quality
left testisUBERON:000453378.75gold quality
prostate glandUBERON:000236778.71gold quality
small intestine Peyer’s patchUBERON:000345478.68gold quality
testisUBERON:000047378.08gold quality
right ovaryUBERON:000211876.84gold quality
small intestineUBERON:000210876.68gold quality
left ovaryUBERON:000211976.59gold quality
body of uterusUBERON:000985376.59gold quality
right lobe of liverUBERON:000111476.37gold quality
subcutaneous adipose tissueUBERON:000219076.31gold quality
ovaryUBERON:000099275.99gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.58

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting SAPCD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-60799.9773.625593
HSA-MIR-365899.9673.874379
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-95-5P99.8972.173973
HSA-MIR-129-5P99.8870.263273
HSA-MIR-3680-3P99.7572.513095
HSA-MIR-5004-5P99.6866.631294
HSA-MIR-317599.6566.302031
HSA-MIR-4666B99.6468.691282
HSA-MIR-432899.5771.064094
HSA-MIR-516B-5P99.5666.331495
HSA-MIR-608199.4866.071446
HSA-MIR-1224-5P99.4865.59803
HSA-MIR-1213199.4868.721673
HSA-MIR-1211399.3267.541072
HSA-MIR-478499.1567.411733
HSA-MIR-442498.9170.331145
HSA-MIR-3150B-3P98.8167.211728
HSA-MIR-6878-5P98.4967.912142
HSA-MIR-4733-3P98.3565.20994
HSA-MIR-876-5P97.9968.491345
HSA-MIR-6783-5P97.6767.211528
HSA-MIR-6824-5P97.4168.43583
HSA-MIR-505-5P97.0165.54778
HSA-MIR-316796.8167.091236
HSA-MIR-345-5P96.4066.43663

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusSapcd1ENSMUSG00000036185
rattus_norvegicusSapcd1ENSRNOG00000000858
drosophila_melanogasterCG3880FBGN0035057
caenorhabditis_elegansWBGENE00020134

Paralogs (1): SAPCD2 (ENSG00000186193)

Protein

Protein identifiers

Suppressor APC domain-containing protein 1 — Q5SSQ6 (reviewed: Q5SSQ6)

Alternative names: Protein G7d

All UniProt accessions (2): Q5SSQ6, A0A1U9X8I8

Isoforms (2)

UniProt IDNamesCanonical?
Q5SSQ6-11yes
Q5SSQ6-22

RefSeq proteins (1): NP_001034740* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR026828SAPC2_1/2Family

Pfam: PF11414

UniProt features (5 total): sequence variant 2, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5SSQ6-F175.980.29

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 104 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP, BOYLAN_MULTIPLE_MYELOMA_C_D_UP, MIKKELSEN_ES_LCP_WITH_H3K4ME3, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, FOSTER_KDM1A_TARGETS_UP, GSE5503_MLN_DC_VS_PLN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, GSE5503_MLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, GSE10240_CTRL_VS_IL17_AND_IL22_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP, MIR4328, MIR6081, MIR5004_5P, MIR345_5P, MIR505_5P

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding1

Protein interactions and networks

STRING

280 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SAPCD1VWA7Q9Y334570
SAPCD1PLEKHG5O94827560
SAPCD1OR2H1Q9GZK4547
SAPCD1ZNF391Q9UJN7542
SAPCD1PSORS1C2Q9UIG4504
SAPCD1P2RX5Q93086475
SAPCD1FKBP10Q96AY3471
SAPCD1C14orf93Q9H972447
SAPCD1ANXA3P12429400
SAPCD1LY6G6CO95867390
SAPCD1FAM241AQ8N8J7373
SAPCD1MSH5O43196371
SAPCD1LY6G6FQ5SQ64362
SAPCD1OR12D2P58182360
SAPCD1NELFEP18615350

IntAct

124 interactions, top by confidence:

ABTypeScore
SAPCD1ARHGAP21psi-mi:“MI:0407”(direct interaction)0.590
SAPCD1PATJpsi-mi:“MI:0407”(direct interaction)0.440
SAPCD1MAGI2psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1MAGI3psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1PDZD7psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1DLG1psi-mi:“MI:0407”(direct interaction)0.440
MAST2SAPCD1psi-mi:“MI:0407”(direct interaction)0.440
DLG4SAPCD1psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1TAMALINpsi-mi:“MI:0407”(direct interaction)0.440
SAPCD1GRID2IPpsi-mi:“MI:0407”(direct interaction)0.440
SAPCD1DLG2psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1DLG4psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1APBA1psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1SNTB1psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1DLG3psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1MPDZpsi-mi:“MI:0407”(direct interaction)0.440
SAPCD1SNTA1psi-mi:“MI:0407”(direct interaction)0.440
DLG1SAPCD1psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1SHANK1psi-mi:“MI:0407”(direct interaction)0.440
SYNJ2BPSAPCD1psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1ARHGEF12psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1NOS1psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1GOPCpsi-mi:“MI:0407”(direct interaction)0.440
SAPCD1MAGI1psi-mi:“MI:0407”(direct interaction)0.440
SAPCD1SNTG2psi-mi:“MI:0407”(direct interaction)0.440

BioGRID (26): CTNNA2 (Affinity Capture-MS), ARHGAP21 (Affinity Capture-MS), ARHGAP23 (Affinity Capture-MS), RANGRF (Affinity Capture-MS), CTNNB1 (Affinity Capture-MS), ARHGAP21 (Affinity Capture-MS), ARHGAP23 (Affinity Capture-MS), RANGRF (Affinity Capture-MS), CTNNA2 (Affinity Capture-MS), CTNNB1 (Affinity Capture-MS), CTNNA1 (Affinity Capture-MS), SAPCD1 (Affinity Capture-RNA), SAPCD1 (Two-hybrid), SAPCD1 (Two-hybrid), SAPCD1 (Two-hybrid)

ESM2 similar proteins: A0A087WVF3, A0A087WXS9, A0A087X179, A0A087X1G2, A6NDS4, A6NER0, A6QPT6, B9A6J9, M3WHG5, O14771, O15482, O15553, O19110, O76081, P0C7X1, P0C7X3, P0C7X4, P35125, P48778, P48967, P79209, Q13670, Q15697, Q2TBC4, Q3T191, Q3UZD7, Q4R2Z8, Q5DRQ5, Q5SSQ6, Q5XFX8, Q69ZB3, Q6DHY5, Q6IPX1, Q6ZMN8, Q8BLR5, Q8BWA8, Q8IYF1, Q8IZP1, Q8JZW5, Q8N7G0

Diamond homologs: Q5SSQ6, Q86UD0, Q9CY86, Q9D818

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 79 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Ras activation upon Ca2+ influx through NMDA receptor553.9×1e-06
Unblocking of NMDA receptors, glutamate binding and activation551.3×1e-06
Negative regulation of NMDA receptor-mediated neuronal transmission551.3×1e-06
Assembly and cell surface presentation of NMDA receptors1047.9×6e-13
Dopamine Neurotransmitter Release Cycle546.8×2e-06
Long-term potentiation544.9×2e-06
Neurexins and neuroligins1140.9×3e-13
Protein-protein interactions at synapses735.1×7e-08

GO biological processes:

GO termPartnersFoldFDR
establishment or maintenance of epithelial cell apical/basal polarity1075.5×2e-14
protein localization to synapse659.7×9e-08
receptor clustering756.7×7e-09
regulation of postsynaptic membrane neurotransmitter receptor levels638.6×8e-07
protein-containing complex assembly913.3×2e-06
cell-cell adhesion1013.2×4e-07
regulation of small GTPase mediated signal transduction59.3×4e-03
protein localization to plasma membrane68.5×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

923 predictions. Top by Δscore:

VariantEffectΔscore
6:31763165:TTGGG:Tdonor_loss1.0000
6:31763167:GG:Gdonor_gain1.0000
6:31763168:GG:Gdonor_gain1.0000
6:31763169:GTGA:Gdonor_loss1.0000
6:31764264:A:AGacceptor_gain1.0000
6:31764265:G:GGacceptor_gain1.0000
6:31763164:TTTGG:Tdonor_gain0.9900
6:31763165:TTGG:Tdonor_gain0.9900
6:31763169:G:GGdonor_gain0.9900
6:31763170:T:Gdonor_loss0.9900
6:31763171:GAG:Gdonor_loss0.9900
6:31763413:A:AGacceptor_gain0.9900
6:31763414:G:GAacceptor_gain0.9900
6:31763414:GC:Gacceptor_gain0.9900
6:31763414:GCT:Gacceptor_gain0.9900
6:31763414:GCTAC:Gacceptor_gain0.9900
6:31763513:G:GTdonor_gain0.9900
6:31763552:TGAGG:Tdonor_loss0.9900
6:31763553:GAGGT:Gdonor_loss0.9900
6:31763554:AGGTA:Adonor_loss0.9900
6:31763555:GGT:Gdonor_loss0.9900
6:31763557:T:Gdonor_loss0.9900
6:31764265:G:GAacceptor_gain0.9900
6:31763166:TGG:Tdonor_gain0.9800
6:31763167:GGG:Gdonor_gain0.9800
6:31763172:AGTAT:Adonor_loss0.9800
6:31763412:CA:Cacceptor_loss0.9800
6:31763414:G:GGacceptor_gain0.9800
6:31763414:GCTA:Gacceptor_gain0.9800
6:31763514:G:Tdonor_gain0.9800

AlphaMissense

1146 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:31763157:T:CF35L0.939
6:31763159:C:AF35L0.939
6:31763159:C:GF35L0.939
6:31764116:T:CI103T0.930
6:31764137:T:CL110S0.929
6:31763438:G:CE46D0.928
6:31763438:G:TE46D0.928
6:31763463:G:CG55R0.906
6:31763437:A:TE46V0.903
6:31763426:G:AM42I0.894
6:31763426:G:CM42I0.894
6:31763426:G:TM42I0.894
6:31763425:T:CM42T0.885
6:31763160:T:CF36L0.882
6:31763162:C:AF36L0.882
6:31763162:C:GF36L0.882
6:31763496:T:CF66L0.880
6:31763498:T:AF66L0.880
6:31763498:T:GF66L0.880
6:31764116:T:GI103S0.861
6:31763464:G:AG55D0.836
6:31763416:T:CL39P0.834
6:31763473:T:CL58P0.826
6:31763447:G:CQ49H0.818
6:31763447:G:TQ49H0.818
6:31764067:T:CF87L0.816
6:31764069:T:AF87L0.816
6:31764069:T:GF87L0.816
6:31763448:G:CD50H0.804
6:31763509:T:CL70P0.804

dbSNP variants (sampled 300 via entrez): RS1001668923 (6:31761838 T>C), RS1003393864 (6:31763425 T>A), RS1004034887 (6:31763111 G>A,C), RS1006120529 (6:31764975 C>T), RS1006483649 (6:31763546 C>A), RS1006864594 (6:31765014 C>G,T), RS1009296444 (6:31761048 A>G), RS1010076963 (6:31760998 C>T), RS1010770999 (6:31764903 C>T), RS1011061316 (6:31762634 G>A), RS1012995215 (6:31763963 C>A,G,T), RS1013103927 (6:31761661 T>G), RS1015875466 (6:31763114 G>A,T), RS1017138945 (6:31764994 T>C), RS1017648727 (6:31761054 C>A,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

27 associations (top):

StudyTraitp-value
GCST003450_2Clozapine-induced agranulocytosis/granulocytopenia in treatment-resistant schizophrenia3.000000e-09
GCST004131_25Inflammatory bowel disease2.000000e-31
GCST004133_79Ulcerative colitis5.000000e-65
GCST004521_114Autism spectrum disorder or schizophrenia3.000000e-17
GCST004521_117Autism spectrum disorder or schizophrenia3.000000e-15
GCST004521_126Autism spectrum disorder or schizophrenia2.000000e-10
GCST004521_154Autism spectrum disorder or schizophrenia3.000000e-08
GCST004521_17Autism spectrum disorder or schizophrenia2.000000e-12
GCST004521_209Autism spectrum disorder or schizophrenia5.000000e-16
GCST004521_211Autism spectrum disorder or schizophrenia5.000000e-15
GCST004521_213Autism spectrum disorder or schizophrenia5.000000e-13
GCST004521_224Autism spectrum disorder or schizophrenia5.000000e-10
GCST004521_227Autism spectrum disorder or schizophrenia4.000000e-12
GCST004521_265Autism spectrum disorder or schizophrenia7.000000e-14
GCST004521_281Autism spectrum disorder or schizophrenia5.000000e-09
GCST004521_296Autism spectrum disorder or schizophrenia6.000000e-18
GCST004521_45Autism spectrum disorder or schizophrenia2.000000e-16
GCST004521_70Autism spectrum disorder or schizophrenia8.000000e-20
GCST004521_81Autism spectrum disorder or schizophrenia1.000000e-14
GCST006228_4Systolic blood pressure6.000000e-08
GCST006230_2Pulse pressure3.000000e-09
GCST006575_37Takayasu arteritis8.000000e-08
GCST006950_12Feeling worry2.000000e-08
GCST008916_111Asthma2.000000e-14
GCST008916_30Asthma1.000000e-09
GCST008917_2Asthma (childhood onset)4.000000e-07
GCST008921_1Asthma and major depressive disorder2.000000e-16

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0006335systolic blood pressure
EFO:0005763pulse pressure measurement
EFO:0009589worry measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, decreases methylation2
Tobacco Smoke Pollutiondecreases expression2
Valproic Acidaffects expression, increases expression2
GSK-J4decreases expression1
2,5,2’,5’-tetrachlorobiphenyldecreases expression1
trichostatin Aincreases expression1
sodium arseniteincreases expression1
butyraldehydedecreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amideincreases expression1
jinfukangincreases expression1
Sunitinibdecreases expression1
Diethylhexyl Phthalatedecreases expression1
Plant Oilsdecreases expression1
Smokedecreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Cyclosporinedecreases expression1
Lactic Aciddecreases expression1
Acrylamidedecreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): childhood onset asthma, Takayasu arteritis

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