FAM163A

gene
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Also known as MGC16664NDSP

Summary

FAM163A (family with sequence similarity 163 member A, HGNC:28274) is a protein-coding gene on chromosome 1q25.2, encoding Protein FAM163A (Q96GL9).

Predicted to be located in membrane.

Source: NCBI Gene 148753 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 32 total
  • Phenotypes (HPO): 1
  • MANE Select transcript: NM_173509

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28274
Approved symbolFAM163A
Namefamily with sequence similarity 163 member A
Location1q25.2
Locus typegene with protein product
StatusApproved
AliasesMGC16664, NDSP
Ensembl geneENSG00000143340
Ensembl biotypeprotein_coding
OMIM611727
Entrez148753

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000341785, ENST00000879738, ENST00000879739

RefSeq mRNA: 18 — MANE Select: NM_173509 NM_001329712, NM_001329713, NM_001329714, NM_001329715, NM_001329716, NM_001329717, NM_001329718, NM_001329719, NM_001393415, NM_001393416, NM_001393417, NM_001393418, NM_001393419, NM_001393420, NM_001393421, NM_001393422, NM_001393423, NM_173509

CCDS: CCDS1333

Canonical transcript exons

ENST00000341785 — 5 exons

ExonStartEnd
ENSE00001372978179813076179813190
ENSE00001381942179812110179812131
ENSE00001405816179743291179743423
ENSE00001445160179813779179816198
ENSE00002395650179807798179807888

Expression profiles

Bgee: expression breadth ubiquitous, 123 present calls, max score 91.84.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4711 / max 120.8767, expressed in 100 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
69200.292364
69210.086431
69190.042416
69180.01838
69160.01673
69170.01505

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001991.84gold quality
male germ cellCL:000001589.42gold quality
pituitary glandUBERON:000000784.98gold quality
adenohypophysisUBERON:000219682.41gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.61gold quality
lateral nuclear group of thalamusUBERON:000273676.51gold quality
right testisUBERON:000453476.09gold quality
left testisUBERON:000453375.65gold quality
ponsUBERON:000098873.35gold quality
testisUBERON:000047373.10gold quality
thymusUBERON:000237068.91gold quality
islet of LangerhansUBERON:000000668.42gold quality
prefrontal cortexUBERON:000045167.54gold quality
right frontal lobeUBERON:000281063.22gold quality
muscle layer of sigmoid colonUBERON:003580562.59gold quality
pigmented layer of retinaUBERON:000178262.54gold quality
cingulate cortexUBERON:000302762.16gold quality
anterior cingulate cortexUBERON:000983562.16gold quality
frontal cortexUBERON:000187061.99gold quality
vermiform appendixUBERON:000115461.34gold quality
neocortexUBERON:000195060.62gold quality
dorsolateral prefrontal cortexUBERON:000983460.61gold quality
Brodmann (1909) area 9UBERON:001354060.42gold quality
olfactory bulbUBERON:000226460.17gold quality
type B pancreatic cellCL:000016959.99gold quality
gall bladderUBERON:000211058.96gold quality
caecumUBERON:000115358.02gold quality
apex of heartUBERON:000209857.23gold quality
cerebral cortexUBERON:000095655.77gold quality
colonUBERON:000115555.20gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

89 targeting FAM163A, 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-6867-5P100.0082.213464
HSA-MIR-4283100.0066.422097
HSA-MIR-4455100.0065.481587
HSA-MIR-453199.9969.703181
HSA-MIR-118499.9968.191458
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-7152-3P99.9767.47849
HSA-MIR-185-3P99.9567.011743
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-449299.8768.253611
HSA-MIR-391999.8769.452489
HSA-MIR-3151-5P99.8663.831069
HSA-MIR-469899.8471.414303
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-1213099.7565.47452
HSA-MIR-6752-3P99.7266.711587
HSA-MIR-4446-5P99.7269.192544
HSA-MIR-378G99.7164.901106
HSA-MIR-4755-5P99.7170.342716
HSA-MIR-5006-3P99.7170.262728
HSA-MIR-670-5P99.6769.941565
HSA-MIR-4756-3P99.6266.301319
HSA-MIR-451699.6167.783390
HSA-MIR-76299.5866.611994
HSA-MIR-105-5P99.5469.242060
HSA-MIR-7853-5P99.5469.302055
HSA-MIR-448999.5065.56785
HSA-MIR-143-3P99.4969.051457
HSA-MIR-477099.4969.091451
HSA-MIR-449899.4767.422360

Literature-anchored findings (GeneRIF, showing 2)

  • NDSP is specifically overexpressed in neuroblastoma and actively secreted from tumor cells. Furthermore, NDSP serves as a growth factor for neuroblastoma tumor cells through activation of the ERK-mediated proliferation pathway. (PMID:19671756)
  • Novel loci for ocular axial length identified through extreme-phenotype genome-wide association study in Chinese populations. (PMID:37524447)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriofam163aaENSDARG00000077470
danio_reriofam163abENSDARG00000093021
mus_musculusFam163aENSMUSG00000015484
rattus_norvegicusFam163aENSRNOG00000024825

Protein

Protein identifiers

Protein FAM163AQ96GL9 (reviewed: Q96GL9)

Alternative names: Cebelin, Neuroblastoma-derived secretory protein

All UniProt accessions (1): Q96GL9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Highly expressed in neuroblastoma compared to other tissues, suggesting that it may be used as a marker for metastasis in bone marrow.

Similarity. Belongs to the FAM163 family.

RefSeq proteins (18): NP_001316641, NP_001316642, NP_001316643, NP_001316644, NP_001316645, NP_001316646, NP_001316647, NP_001316648, NP_001380344, NP_001380345, NP_001380346, NP_001380347, NP_001380348, NP_001380349, NP_001380350, NP_001380351, NP_001380352, NP_775780* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR029379FAM163Family
IPR040281FAM163AFamily

Pfam: PF15069

UniProt features (2 total): chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96GL9-F158.540.10

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 56 (showing top): BENPORATH_ES_WITH_H3K27ME3, chr1q25, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, GSE13522_CTRL_VS_T_CRUZI_G_STRAIN_INF_SKIN_DN, MIR6867_5P, MIR4492, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2, MIR4283, MIR185_3P, MIR6752_3P, MIR6814_5P, MIR571

GO Biological Process (0):

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

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

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding1
cellular anatomical structure1

Protein interactions and networks

STRING

516 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FAM163ALRP10Q7Z4F1553
FAM163ADCAF13Q9NV06480
FAM163ACST9LQ9H4G1474
FAM163ATOR1AIP2Q8NFQ8468
FAM163ALRP4O75096466
FAM163AMAMDC2Q7Z304462
FAM163ACSKMTA8MUP2448
FAM163AV9GXZ4V9GXZ4435
FAM163AFRAS1Q86XX4428
FAM163ATOR1AIP1Q5JTV8422
FAM163ATNNI3KQ59H18419
FAM163APVRIGQ6DKI7418
FAM163ATAFA1Q7Z5A9413
FAM163ACACFD1Q9UGQ2408
FAM163ACCBE1Q6UXH8405

IntAct

75 interactions, top by confidence:

ABTypeScore
GET3FAM163Apsi-mi:“MI:0915”(physical association)0.560
RWDD2BFAM163Apsi-mi:“MI:0915”(physical association)0.560
TMEM179BFAM163Apsi-mi:“MI:0915”(physical association)0.560
GAD2FAM163Apsi-mi:“MI:0915”(physical association)0.560
CRYAAFAM163Apsi-mi:“MI:0915”(physical association)0.560
FAM163AATN1psi-mi:“MI:0915”(physical association)0.560
FAM163AF13A1psi-mi:“MI:0915”(physical association)0.560
FAM163AFGFR3psi-mi:“MI:0915”(physical association)0.560
GRIN2CFAM163Apsi-mi:“MI:0915”(physical association)0.560
FAM163AGSNpsi-mi:“MI:0915”(physical association)0.560
UBE2KFAM163Apsi-mi:“MI:0915”(physical association)0.560
FAM163AHSPB1psi-mi:“MI:0915”(physical association)0.560
FAM163APECAM1psi-mi:“MI:0915”(physical association)0.560
FAM163AVIMpsi-mi:“MI:0915”(physical association)0.560
FAM163AWFS1psi-mi:“MI:0915”(physical association)0.560
FAM163AGIPC1psi-mi:“MI:0915”(physical association)0.560
FAM163AKIF1Bpsi-mi:“MI:0915”(physical association)0.560
FAM163ARNF11psi-mi:“MI:0915”(physical association)0.560
UBQLN1FAM163Apsi-mi:“MI:0915”(physical association)0.560
HTTFAM163Apsi-mi:“MI:0915”(physical association)0.560

BioGRID (23): WDR47 (Affinity Capture-MS), YWHAZ (Affinity Capture-MS), YWHAG (Affinity Capture-MS), YWHAE (Affinity Capture-MS), YWHAB (Affinity Capture-MS), FAM163A (Two-hybrid), RWDD2B (Two-hybrid), TMEM179B (Two-hybrid), WDR47 (Affinity Capture-MS), YWHAG (Affinity Capture-MS), YWHAZ (Affinity Capture-MS), CRTAP (Affinity Capture-MS), KLHL22 (Affinity Capture-MS), FAM163A (Affinity Capture-MS), TRIM68 (Affinity Capture-MS)

ESM2 similar proteins: A1L3I3, A2A699, A2RV66, A4IG66, A6NL88, A6QPA0, A7MC48, A8MVW0, B3DHW5, B4DS77, D3ZD05, D3ZZP4, E9Q0S6, G3V735, J3QNX5, O94983, P0C2L3, Q08E39, Q1LZH7, Q2WFL8, Q3UH99, Q3UIL6, Q5BJT1, Q5BLC7, Q5DU25, Q5JU85, Q5SWY7, Q63ZY3, Q69YU3, Q6IQ23, Q6UWI4, Q6ZSJ9, Q7T0Z7, Q80Y50, Q8BUM6, Q8BX02, Q8C3Q5, Q8C8T7, Q8CAA5, Q8IUW5

Diamond homologs: P0C2L3, Q0VFM5, Q8BUM6, Q8CAA5, Q96GL9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance29
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1980 predictions. Top by Δscore:

VariantEffectΔscore
1:179807889:G:GGdonor_gain1.0000
1:179809405:GGAAT:Gdonor_gain1.0000
1:179809406:GAATG:Gdonor_gain1.0000
1:179809407:A:Tdonor_gain1.0000
1:179809417:C:Gdonor_gain1.0000
1:179813777:A:AGacceptor_gain1.0000
1:179813778:G:GGacceptor_gain1.0000
1:179813778:GT:Gacceptor_gain1.0000
1:179743390:G:GTdonor_gain0.9900
1:179743452:G:Tdonor_gain0.9900
1:179807796:AG:Aacceptor_gain0.9900
1:179807797:GG:Gacceptor_gain0.9900
1:179807887:ACGT:Adonor_loss0.9900
1:179807888:CGTA:Cdonor_loss0.9900
1:179807889:G:GAdonor_loss0.9900
1:179807890:T:TGdonor_loss0.9900
1:179807891:A:AGdonor_loss0.9900
1:179807893:GT:Gdonor_gain0.9900
1:179809447:G:GGdonor_gain0.9900
1:179812132:G:GGdonor_gain0.9900
1:179813075:GA:Gacceptor_gain0.9900
1:179813776:C:Gacceptor_gain0.9900
1:179813776:CA:Cacceptor_loss0.9900
1:179813777:A:Gacceptor_loss0.9900
1:179813778:GTA:Gacceptor_gain0.9900
1:179813778:GTATT:Gacceptor_gain0.9900
1:179743907:G:GTdonor_gain0.9800
1:179743907:G:Tdonor_gain0.9800
1:179807792:TGGCA:Tacceptor_loss0.9800
1:179807793:GGCA:Gacceptor_loss0.9800

AlphaMissense

1074 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:179813126:G:AG10D0.996
1:179813125:G:CG10R0.994
1:179813150:T:AL18H0.994
1:179813128:G:AG11R0.992
1:179813128:G:CG11R0.992
1:179813138:C:AA14D0.992
1:179813155:T:CC20R0.989
1:179813173:T:CC26R0.989
1:179813120:T:AI8N0.987
1:179813129:G:AG11E0.987
1:179813107:G:AG4R0.986
1:179813107:G:CG4R0.986
1:179813114:T:AV6D0.986
1:179813150:T:GL18R0.986
1:179814175:A:CS164R0.986
1:179814177:T:AS164R0.986
1:179814177:T:GS164R0.986
1:179813153:T:AL19H0.985
1:179813147:T:AI17N0.983
1:179813153:T:GL19R0.983
1:179813183:G:TR29M0.983
1:179813179:T:CC28R0.982
1:179813141:C:AT15K0.980
1:179813102:C:TT2I0.976
1:179813108:G:AG4E0.976
1:179813181:C:GC28W0.976
1:179813180:G:AC28Y0.975
1:179813120:T:GI8S0.974
1:179813120:T:CI8T0.972
1:179813135:T:GL13R0.972

dbSNP variants (sampled 300 via entrez): RS1000062655 (1:179781370 C>T), RS1000066720 (1:179811085 A>C,T), RS1000088794 (1:179806689 G>A,C,T), RS1000097335 (1:179766230 A>G), RS1000143810 (1:179765071 T>C), RS1000150240 (1:179739345 A>G), RS1000159423 (1:179794130 G>C,T), RS1000177829 (1:179789311 A>G), RS1000255495 (1:179743950 G>T), RS1000297288 (1:179774411 A>G), RS1000307480 (1:179800558 T>G), RS1000314797 (1:179782756 G>A), RS1000361383 (1:179775015 G>A,C), RS1000419080 (1:179746363 T>A,C), RS1000446428 (1:179765990 G>A)

Disease associations

OMIM: gene MIM:611727 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): endometriosis (MONDO:0005133)

Orphanet (0):

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPOTerm
HP:0030127Endometriosis

GWAS associations

3 associations (top):

StudyTraitp-value
GCST008810_37Smoking initiation (ever regular vs never regular)1.000000e-07
GCST009441_11Age-related cognitive decline (memory) (slope of z-scores)3.000000e-06
GCST90002394_91Monocyte percentage of white cells4.000000e-10

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0005670smoking initiation
EFO:0007710cognitive decline measurement
EFO:0007989monocyte percentage of leukocytes

MeSH disease descriptors (1)

DescriptorNameTree numbers
D004715EndometriosisC12.050.351.500.163; C12.100.250.163

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 Acidaffects cotreatment, decreases expression, decreases methylation2
Aflatoxin B1decreases methylation2
bisphenol Adecreases methylation1
arseniteincreases methylation1
aflatoxin B2increases methylation1
entinostatincreases expression1
(+)-JQ1 compoundaffects expression, increases reaction1
Resveratroldecreases expression, affects cotreatment1
Fulvestrantincreases methylation1
Panobinostatincreases reaction, affects expression1
Atrazinedecreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Copperdecreases expression, affects cotreatment1
Diethylhexyl Phthalatedecreases expression1
Folic Aciddecreases expression1
Hydralazineaffects cotreatment, decreases expression1
Silicon Dioxidedecreases expression1
Dronabinoldecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Triclosanincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00286351PHASE4COMPLETEDUse of Arimidex and Zoladex as Pretreatment to IVF in Women With Ovarian Endometriosis
NCT00621179PHASE4COMPLETEDEndometrial Markers and Response of Endometriosis Patients to Prolonged GnRH Agonist Prior to IVF
NCT00625950PHASE4COMPLETEDEndometriosis Patients Undergoing Quinagolide Treatment
NCT00654524PHASE4UNKNOWNRandomized Study of Gonadotropin-releasing-hormone Agonist (GnRH-a) or Expectant Management for Endometriosis
NCT00735852PHASE4COMPLETEDDecapeptyl SR With Livial Add Back Therapy in the Management of Chronic Cyclical Pelvic Pain in Pre Menopausal Women
NCT00844012PHASE4UNKNOWNContinuous Postoperative Use of Low-Dose Combined Oral Contraceptivesfor for Endometriosis-Related Chronic Pelvic Pain
NCT01056042PHASE4COMPLETEDEfficacy of Injectable Contraceptive and Oral Contraceptive Administered After Surgical Treatment of Endometriosis With Pain
NCT01581359PHASE4COMPLETEDThe Effect of Pre-treatment With GnRH Analogues Prior in Vitro Fertilization in Patients With Endometriosis
NCT01682642PHASE4COMPLETEDThe Influence of Adjuvant Medical Treatment of Peritoneal Endometriosis on the Outcome of IVF. A Prospective Randomized Analysis.
NCT01769781PHASE4COMPLETEDAnastrazole Plus GnRH-agonist in the Treatment of Endometriosis Recurrence
NCT01779232PHASE4COMPLETEDDanazol Treatment in Endometriosis Women Before IVF
NCT02158845PHASE4COMPLETEDLevonorgestrel-releasing Intrauterine System in Patients With Endometriosis
NCT02165917PHASE4UNKNOWNStudy to Compare Peritoneal Ablation by Excision Only and Excision With the Use of an Adhesion Barrier
NCT02213081PHASE4COMPLETEDUlipristal for Endometriosis-related Pelvic Pain
NCT02214550PHASE4COMPLETEDChronic Pain Risk Associated With Menstrual Period Pain
NCT02385448PHASE4UNKNOWNComparing the Use of Dienogest and Combined Oral Contraceptive Pills (Microgynon) to Reduce the Risk of Recurrence of Endometriotic Cyst After Conservative Surgery
NCT02387931PHASE4COMPLETEDSupplementation in Adolescent Girls With Endometriosis
NCT02393482PHASE4UNKNOWNPsychological Impact of Amenorrhea in Women With Endometriosis
NCT02427386PHASE4COMPLETEDHomeopathic Treatment of Chronic Pelvic Pain in Women With Endometriosis
NCT02475564PHASE4COMPLETEDResveratrol for Pain Due to Endometriosis
NCT02480647PHASE4COMPLETEDClinical Trial the Use of Levonorgestrel-releasing Intrauterine System Versus Etonogestrel Implant in Endometriosis
NCT02534688PHASE4COMPLETEDEffectiveness of Levonorgestrel-intrauterine System (LNG-IUS) Versus Depot Medroxyprogesterone Acetate (DMPA) in Treatment of Pelvic Pain in Clinically Diagnosed Endometriotic Patients
NCT02812186PHASE4COMPLETEDDeep Versus Moderate Neuromuscular Blockade During Laparoscopic Surgery
NCT04218487PHASE4UNKNOWNXuefu-Zhuyu Capsule for the Treatment of Qizhi Xueyu Zheng (Qi Stagnation and Blood Stasis Syndrome)
NCT04554693PHASE4ACTIVE_NOT_RECRUITINGThe Use of Low Dose Metronidazole to Decrease Postoperative Pain After Endometriosis Surgery
NCT04942015PHASE4UNKNOWNHonghuaruyi Wan for Endometriosis Dysmenorrhea
NCT05013242PHASE4UNKNOWNGoserline Acetate VS Dienogest in Endometriosi
NCT05059626PHASE4RECRUITINGEndometriosis and Microvascular Dysfunction; Simvastatin and Duavee
NCT05331053PHASE4TERMINATEDMicroRNA Activation of LOX-1 Mechanisms in Endometriosis
NCT05560230PHASE4COMPLETEDIntraoperative Clonidine for Postoperative Pain Management in Patients Undergoing Surgical Treatment for Endometriosis
NCT05962034PHASE4RECRUITINGThromboxane Function in Women With Endometriosis
NCT06523530PHASE4RECRUITINGEffect of a GnRH Analog on Hepatic Steatosis
NCT06543550PHASE4RECRUITINGComparison Between the Effects of Implantable Gestrinone and Oral Dienogest in the Treatment of Endometriosis
NCT06577233PHASE4RECRUITINGSuperior Hypogastric Nerve Plexus Block With Bupivacaine After Robotic Resection of Endometriosis
NCT06951802PHASE4RECRUITINGEndometriosis and Pain Treatment by Intraoperative Administration of Low-dose Ketamine
NCT07144904PHASE4NOT_YET_RECRUITINGAssessing the Efficacy of Indocyanine Green for Ureter Identification During Robot-Assisted Surgery in Advanced-Stage Endometriosis
NCT07182032PHASE4WITHDRAWNKetamine in Central Sensitization
NCT07532876PHASE4ENROLLING_BY_INVITATIONComparison of Elagolix and OCPs in Reducing Endometriosis Associated Pelvic Pain
NCT00225186PHASE3COMPLETEDSafety and Efficacy of SH T00660AA in Treatment of Endometriosis
NCT00225199PHASE3COMPLETEDEfficacy and Safety of SH T00660AA in Treatment of Endometriosis
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): endometriosis