ARL6IP6

gene
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Also known as MGC33864

Summary

ARL6IP6 (ARF like GTPase 6 interacting protein 6, HGNC:24048) is a protein-coding gene on chromosome 2q23.3, encoding ADP-ribosylation factor-like protein 6-interacting protein 6 (Q8N6S5).

Predicted to be located in nuclear inner membrane.

Source: NCBI Gene 151188 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): cutis marmorata telangiectatica congenita (Limited, GenCC)
  • GWAS associations: 4
  • Clinical variants (ClinVar): 48 total — 1 likely-pathogenic
  • Phenotypes (HPO): 32
  • MANE Select transcript: NM_152522

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24048
Approved symbolARL6IP6
NameARF like GTPase 6 interacting protein 6
Location2q23.3
Locus typegene with protein product
StatusApproved
AliasesMGC33864
Ensembl geneENSG00000177917
Ensembl biotypeprotein_coding
OMIM616495
Entrez151188

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 11 protein_coding, 5 retained_intron, 4 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined

ENST00000326446, ENST00000425034, ENST00000455875, ENST00000463690, ENST00000495469, ENST00000685752, ENST00000686080, ENST00000686839, ENST00000686951, ENST00000687504, ENST00000688012, ENST00000688130, ENST00000688171, ENST00000688293, ENST00000689155, ENST00000690119, ENST00000690703, ENST00000690727, ENST00000691523, ENST00000691702, ENST00000692124, ENST00000692399, ENST00000693573

RefSeq mRNA: 3 — MANE Select: NM_152522 NM_001350068, NM_001371972, NM_152522

CCDS: CCDS2197, CCDS92880

Canonical transcript exons

ENST00000326446 — 4 exons

ExonStartEnd
ENSE00001288604152759747152762396
ENSE00001288614152718620152719024
ENSE00003467576152734994152735126
ENSE00003493000152720533152720586

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 98.15.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.1533 / max 315.5645, expressed in 1819 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
2310333.58381817
231023.55451565
231011.4207744
231050.304886
231040.2895111

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305398.15gold quality
ganglionic eminenceUBERON:000402397.63gold quality
germinal epithelium of ovaryUBERON:000130496.51gold quality
trabecular bone tissueUBERON:000248395.67gold quality
placentaUBERON:000198794.67gold quality
epithelial cell of pancreasCL:000008394.53gold quality
skin of hipUBERON:000155494.12gold quality
palpebral conjunctivaUBERON:000181294.03gold quality
upper leg skinUBERON:000426294.01gold quality
oral cavityUBERON:000016793.39gold quality
parietal pleuraUBERON:000240092.59gold quality
bronchial epithelial cellCL:000232892.39gold quality
oviduct epitheliumUBERON:000480492.39gold quality
bone marrowUBERON:000237192.27gold quality
mammalian vulvaUBERON:000099792.22gold quality
mucosa of sigmoid colonUBERON:000499391.98gold quality
epithelium of nasopharynxUBERON:000195191.82gold quality
bronchusUBERON:000218591.82gold quality
visceral pleuraUBERON:000240191.75gold quality
colonic mucosaUBERON:000031791.63gold quality
superficial temporal arteryUBERON:000161491.49gold quality
adult organismUBERON:000702391.19gold quality
thymusUBERON:000237091.10gold quality
jejunal mucosaUBERON:000039991.05gold quality
tibiaUBERON:000097990.93gold quality
mucosa of paranasal sinusUBERON:000503090.83gold quality
seminal vesicleUBERON:000099890.74gold quality
lower lobe of lungUBERON:000894990.68gold quality
monocyteCL:000057690.57gold quality
esophagus squamous epitheliumUBERON:000692090.51gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-HCAD-5yes20.95
E-MTAB-7381no224.81
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

128 targeting ARL6IP6, 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-3163100.0077.238605
HSA-MIR-8485100.0077.574731
HSA-MIR-5692A100.0074.406850
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-548N99.9871.944170
HSA-MIR-56899.9869.862084
HSA-MIR-548P99.9872.253784
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-1213699.9872.815713
HSA-MIR-433-3P99.9869.371203
HSA-MIR-60799.9773.625593
HSA-MIR-3605-5P99.9667.12932
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-570-3P99.9672.414910
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-548AR-5P99.9471.283515

Literature-anchored findings (GeneRIF, showing 1)

  • ARL6IP6 as a novel candidate gene for a syndromic form of CMTC. (PMID:25957586)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioarl6ip6ENSDARG00000071013
mus_musculusArl6ip6ENSMUSG00000026960
rattus_norvegicusArl6ip6ENSRNOG00000005074

Protein

Protein identifiers

ADP-ribosylation factor-like protein 6-interacting protein 6Q8N6S5 (reviewed: Q8N6S5)

Alternative names: Phosphonoformate immuno-associated protein 1

All UniProt accessions (9): Q8N6S5, A0A8I5KQ30, A0A8I5KQY4, A0A8I5KRB3, A0A8I5KU55, A0A8I5KYK3, A0A8I5QJ95, H7C0H7, H7C192

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus inner membrane.

Similarity. Belongs to the ARL6IP6 family.

RefSeq proteins (3): NP_001336997, NP_001358901, NP_689735* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR029383ARL6IP6Family

Pfam: PF15062

UniProt features (13 total): modified residue 5, transmembrane region 3, region of interest 2, chain 1, sequence conflict 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N6S5-F156.770.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (5): 65, 80, 2, 36, 60

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 232 (showing top): HORIUCHI_WTAP_TARGETS_DN, FISCHER_G1_S_CELL_CYCLE, LFA1_Q6, CMYB_01, HNF4_01, DODD_NASOPHARYNGEAL_CARCINOMA_UP, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, FISCHER_DREAM_TARGETS, ZHANG_BREAST_CANCER_PROGENITORS_UP, RGAGGAARY_PU1_Q6, GOCC_NUCLEAR_ENVELOPE, NUYTTEN_EZH2_TARGETS_DN, GOCC_ORGANELLE_INNER_MEMBRANE, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED

GO Biological Process (0):

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

GO Cellular Component (3): nuclear inner membrane (GO:0005637), nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding1
organelle inner membrane1
nuclear membrane1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

374 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ARL6IP6FMNL2Q96PY5646
ARL6IP6RFTN2Q52LD8552
ARL6IP6PLBD2Q8NHP8518
ARL6IP6MED29Q9NX70485
ARL6IP6HEMK2Q9Y5N5482
ARL6IP6ATP6V1AP38606425
ARL6IP6FAM177A1Q8N128374
ARL6IP6TMED8Q6PL24371
ARL6IP6ANGEL2Q5VTE6366
ARL6IP6MTIF3Q9H2K0364
ARL6IP6MRPS9P82933351
ARL6IP6RNASE13Q5GAN3337
ARL6IP6SDSP20132333
ARL6IP6PLEKHH2Q8IVE3328
ARL6IP6ARL14EPQ8N8R7326

IntAct

68 interactions, top by confidence:

ABTypeScore
HMOX1psi-mi:“MI:0914”(association)0.740
SLC10A1ARL6IP6psi-mi:“MI:0915”(physical association)0.670
ARL6IP6AQP6psi-mi:“MI:0915”(physical association)0.560
ARL6IP6GPR61psi-mi:“MI:0915”(physical association)0.560
ARL6IP6CMTM2psi-mi:“MI:0915”(physical association)0.560
ARL6IP6TMEM80psi-mi:“MI:0915”(physical association)0.560
AQP6ARL6IP6psi-mi:“MI:0915”(physical association)0.560
EBPARL6IP6psi-mi:“MI:0915”(physical association)0.560
ARL6IP6RUSF1psi-mi:“MI:0915”(physical association)0.560
TMEM205ARL6IP6psi-mi:“MI:0915”(physical association)0.560
GJA8ARL6IP6psi-mi:“MI:0915”(physical association)0.560
ARL6IP6TIMMDC1psi-mi:“MI:0915”(physical association)0.560
CLRN2ARL6IP6psi-mi:“MI:0915”(physical association)0.560
TMEM86BARL6IP6psi-mi:“MI:0915”(physical association)0.560
TBXA2RARL6IP6psi-mi:“MI:0915”(physical association)0.560
MGST3ARL6IP6psi-mi:“MI:0915”(physical association)0.560
SPINT2UPK3BL1psi-mi:“MI:0914”(association)0.530
ARL6IP6YKT6psi-mi:“MI:0914”(association)0.530
AOC3AOC2psi-mi:“MI:0914”(association)0.530
CLEC2BASPHD2psi-mi:“MI:0914”(association)0.530
ARL6IP6DRD2psi-mi:“MI:0915”(physical association)0.370
Bmpr1aPLEKHG3psi-mi:“MI:0914”(association)0.350
PLOD2psi-mi:“MI:0914”(association)0.350
ARL6IP6ARPC1Bpsi-mi:“MI:0914”(association)0.350
ARL6IP6ESYT2psi-mi:“MI:0914”(association)0.350
LPAR1GOSR2psi-mi:“MI:0914”(association)0.350

BioGRID (120): YKT6 (Affinity Capture-MS), DUSP3 (Affinity Capture-MS), PNPO (Affinity Capture-MS), BLVRB (Affinity Capture-MS), GSTM1 (Affinity Capture-MS), CBFB (Affinity Capture-MS), PMVK (Affinity Capture-MS), NME2P1 (Affinity Capture-MS), NAA50 (Affinity Capture-MS), UBE2D2 (Affinity Capture-MS), PYGB (Affinity Capture-MS), SNX3 (Affinity Capture-MS), ARL6IP6 (Affinity Capture-MS), PNPO (Affinity Capture-MS), DUSP3 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GRQ0, A0A1B0GSZ0, A0A1B0GVT2, A0A590UK83, A0PK05, A2VDU1, A2VE22, A4QNL6, A5D7B5, A5D992, O43609, O75324, P0DKX4, P29414, P61807, P61808, Q0VFM5, Q15053, Q16655, Q17Q87, Q1L0X2, Q2KIK3, Q2TBG9, Q3MHM8, Q498C7, Q4V921, Q58CU5, Q5RBD8, Q5RF07, Q5RGQ8, Q64448, Q6UWT2, Q80ZU4, Q8BGN6, Q8BUM6, Q8C3K5, Q8C817, Q8K1D8, Q8N6S5, Q91VT8

Diamond homologs: Q3MHM8, Q68FV2, Q8BH07, Q8N6S5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance38
Likely benign0
Benign2

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
2500155NM_152522.7(ARL6IP6):c.373C>T (p.Leu125Phe)Likely pathogenic

SpliceAI

1580 predictions. Top by Δscore:

VariantEffectΔscore
2:152734991:AAG:Aacceptor_gain1.0000
2:152734992:A:Gacceptor_gain1.0000
2:152735122:TTC:Tdonor_gain1.0000
2:152735124:CAAGT:Cdonor_loss1.0000
2:152735125:AAG:Adonor_loss1.0000
2:152735126:AGT:Adonor_loss1.0000
2:152735127:G:GGdonor_gain1.0000
2:152735127:GTAAG:Gdonor_loss1.0000
2:152735128:TAA:Tdonor_loss1.0000
2:152735129:AAGTA:Adonor_loss1.0000
2:152718016:G:Tdonor_gain0.9900
2:152718020:G:GTdonor_gain0.9900
2:152718043:G:GTdonor_gain0.9900
2:152718043:G:Tdonor_gain0.9900
2:152720531:A:AGacceptor_gain0.9900
2:152720532:G:GGacceptor_gain0.9900
2:152720532:GA:Gacceptor_gain0.9900
2:152720532:GAGTT:Gacceptor_gain0.9900
2:152727179:A:AGdonor_gain0.9900
2:152734987:T:Aacceptor_gain0.9900
2:152734988:GTTAA:Gacceptor_loss0.9900
2:152734989:TTAA:Tacceptor_loss0.9900
2:152734990:TAAG:Tacceptor_loss0.9900
2:152734991:A:AGacceptor_gain0.9900
2:152734993:G:Aacceptor_gain0.9900
2:152734993:G:GCacceptor_loss0.9900
2:152735122:TTCAA:Tdonor_gain0.9900
2:152735123:TCA:Tdonor_gain0.9900
2:152735130:AGTAT:Adonor_loss0.9900
2:152741502:G:GTdonor_gain0.9900

AlphaMissense

1448 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:152735044:A:CS169R0.998
2:152735046:C:AS169R0.998
2:152735046:C:GS169R0.998
2:152735053:T:AW172R0.996
2:152735053:T:CW172R0.996
2:152759799:G:CG214R0.995
2:152759800:G:AG214D0.994
2:152735092:T:CF185L0.993
2:152735094:T:AF185L0.993
2:152735094:T:GF185L0.993
2:152735041:T:CC168R0.992
2:152759781:A:CS208R0.992
2:152759783:C:AS208R0.992
2:152759783:C:GS208R0.992
2:152759798:T:AN213K0.992
2:152759798:T:GN213K0.992
2:152735038:T:CC167R0.991
2:152735029:G:AG164R0.990
2:152735029:G:CG164R0.990
2:152735030:G:AG164E0.990
2:152759766:T:CF203L0.989
2:152759768:C:AF203L0.989
2:152759768:C:GF203L0.989
2:152759778:T:CY207H0.988
2:152735072:A:TD178V0.987
2:152735074:T:CS179P0.987
2:152735065:T:GY176D0.985
2:152759775:G:CG206R0.985
2:152735077:T:CF180L0.983
2:152735079:T:AF180L0.983

dbSNP variants (sampled 300 via entrez): RS1000008360 (2:152715675 C>T), RS1000010697 (2:152752199 T>C), RS1000037764 (2:152760299 C>T), RS1000046795 (2:152720394 T>C), RS1000169314 (2:152745966 T>G), RS1000176764 (2:152760891 G>A), RS1000248823 (2:152720761 G>T), RS1000250326 (2:152752510 T>C), RS1000289351 (2:152725793 T>A), RS1000426507 (2:152716527 T>A,C), RS1000519651 (2:152755348 C>T), RS1000560755 (2:152726195 G>A), RS1000561411 (2:152734480 A>G), RS1000583262 (2:152740474 G>A), RS1000584473 (2:152722181 C>T)

Disease associations

OMIM: gene MIM:616495 | disease phenotypes: MIM:209900

GenCC curated gene-disease

DiseaseClassificationInheritance
cutis marmorata telangiectatica congenitaLimitedAutosomal recessive

Mondo (2): Bardet-Biedl syndrome (MONDO:0015229), cutis marmorata telangiectatica congenita (MONDO:0009055)

Orphanet (1): Bardet-Biedl syndrome (Orphanet:110)

HPO phenotypes

32 total (30 of 32 shown, HPO-id order):

HPOTerm
HP:0000003Multicystic kidney dysplasia
HP:0000202Orofacial cleft
HP:0000347Micrognathia
HP:0000541Retinal detachment
HP:0000555Leukocoria
HP:0000821Hypothyroidism
HP:0000951Abnormality of the skin
HP:0000965Cutis marmorata
HP:0000979Purpura
HP:0001250Seizure
HP:0001511Intrauterine growth retardation
HP:0001541Ascites
HP:0001643Patent ductus arteriosus
HP:0001770Toe syndactyly
HP:0001933Subcutaneous hemorrhage
HP:0002650Scoliosis
HP:0002814Abnormality of the lower limb
HP:0002817Abnormality of the upper limb
HP:0004349Reduced bone mineral density
HP:0005306Capillary hemangioma
HP:0006101Finger syndactyly
HP:0006385Short lower limbs
HP:0007565Multiple cafe-au-lait spots
HP:0008065Aplasia/Hypoplasia of the skin
HP:0100026Arteriovenous malformation
HP:0100543Cognitive impairment
HP:0100545Arterial stenosis
HP:0100555Asymmetric growth
HP:0100585Telangiectasia of the skin
HP:0100627Displacement of the urethral meatus

GWAS associations

4 associations (top):

StudyTraitp-value
GCST004748_71Lung cancer4.000000e-06
GCST005434_30Pancreatic cancer3.000000e-07
GCST010002_400Refractive error6.000000e-11
GCST012303_5Recurrent major depressive disorder x sex interaction5.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0008343sex interaction measurement

MeSH disease descriptors (2)

DescriptorNameTree numbers
D020788Bardet-Biedl SyndromeC10.228.140.617.200; C11.270.684.624; C16.131.077.245.125; C16.320.184.125
C536226Cutis marmorata telangiectatica congenita (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects cotreatment, decreases methylation, decreases expression2
sodium arseniteaffects splicing, decreases expression2
Benzo(a)pyrenedecreases expression, increases expression2
Phenylmercuric Acetatedecreases expression, affects cotreatment2
Valproic Aciddecreases expression, decreases methylation2
Cyclosporinedecreases expression, increases expression2
GSK-J4decreases expression1
FR900359decreases phosphorylation1
triphenyl phosphateaffects expression1
arseniteaffects binding, decreases reaction1
perfluorooctanoic aciddecreases expression1
coumarindecreases phosphorylation1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Acetaminophenincreases expression1
Caffeineincreases phosphorylation1
Calcitriolaffects cotreatment, decreases expression1
Dietary Carbohydratesincreases expression1
Estradioldecreases expression1
Formaldehydedecreases expression1
Testosteronedecreases expression, affects cotreatment1
Tetrachlorodibenzodioxinaffects expression1
Urethaneincreases expression1
Aflatoxin B1decreases methylation1
Cadmium Chloridedecreases expression1
Okadaic Aciddecreases expression1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03746522PHASE3COMPLETEDSetmelanotide (RM-493), Melanocortin-4 Receptor (MC4R) Agonist, in Bardet-Biedl Syndrome (BBS) and Alström Syndrome (AS) Participants With Moderate to Severe Obesity
NCT04966741PHASE3COMPLETEDSetmelanotide in Pediatric Participants With Rare Genetic Diseases of Obesity
NCT05194124PHASE3COMPLETEDPhase 3 Crossover Trial of Two Formulations of Setmelanotide in Participants With Specific Gene Defects in the MC4R Pathway
NCT03490019PHASE2WITHDRAWNTreatment of Bardet-Biedl-Syndrome With Metformin for Evaluation of a Possible Visual Improvement
NCT00078091Not specifiedTERMINATEDGenetics and Clinical Characteristics of Bardet-Biedl Syndrome
NCT00213811Not specifiedCOMPLETEDBardet-Biedl Syndrome Study: Clinical and Genetic Epidemiology Study in Adults
NCT01401998Not specifiedRECRUITINGARPKD Database Study
NCT02329210Not specifiedRECRUITINGClinical Registry Investigating Bardet-Biedl Syndrome
NCT02435940Not specifiedRECRUITINGInherited Retinal Degenerative Disease Registry
NCT04461444Not specifiedRECRUITINGCOhort for Bardet-Bield Syndrome and Alström Syndrome for Translational Research Monocentric Interventional Study
NCT04463316Not specifiedRECRUITINGGROWing Up With Rare GENEtic Syndromes
NCT04874909Not specifiedCOMPLETEDClassification, Functional Stratification and Biomarkers in Ciliopathy (CILLICORIRCM)
NCT05183802Not specifiedAPPROVED_FOR_MARKETINGAn Expanded Access Protocol for Setmelanotide for Treatment of Bardet-Biedl Syndrome (BBS)
NCT05400278Not specifiedCOMPLETEDCharacterizing the Genotype and Phenotype in Adults With Bardet-Biedl Syndrome
NCT06239064Not specifiedACTIVE_NOT_RECRUITINGEarly Genetic Identification of Obesity
NCT06615011Not specifiedNOT_YET_RECRUITINGBardet Beidle Syndrome in a Syrian Adolescent : a Rare Case Report
NCT07602803Not specifiedCOMPLETEDThe Effect of GLP1 Agonists on Weight Loss in BBS Cohort in the UK