AFTPH

gene
On this page

Also known as MGC33965FLJ20080FLJ23793Nbla10388

Summary

AFTPH (aftiphilin, HGNC:25951) is a protein-coding gene on chromosome 2p14, encoding Aftiphilin (Q6ULP2). Component of clathrin-coated vesicles.

Enables clathrin binding activity. Predicted to be involved in intracellular transport. Located in Golgi apparatus; cytosol; and nucleoplasm. Part of AP-1 adaptor complex.

Source: NCBI Gene 54812 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 155 total
  • MANE Select transcript: NM_203437

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25951
Approved symbolAFTPH
Nameaftiphilin
Location2p14
Locus typegene with protein product
StatusApproved
AliasesMGC33965, FLJ20080, FLJ23793, Nbla10388
Ensembl geneENSG00000119844
Ensembl biotypeprotein_coding
OMIM619628
Entrez54812

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 19 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron

ENST00000238856, ENST00000409183, ENST00000409933, ENST00000487769, ENST00000498706, ENST00000695864, ENST00000695865, ENST00000695866, ENST00000695867, ENST00000695868, ENST00000695869, ENST00000695960, ENST00000880238, ENST00000880239, ENST00000880240, ENST00000880241, ENST00000880242, ENST00000880243, ENST00000880244, ENST00000920107, ENST00000920108, ENST00000942373, ENST00000942374

RefSeq mRNA: 10 — MANE Select: NM_203437 NM_001002243, NM_001375969, NM_001375970, NM_001375971, NM_001375972, NM_001375973, NM_001394995, NM_001394996, NM_017657, NM_203437

CCDS: CCDS1878, CCDS46303, CCDS92767, CCDS92768, CCDS92769, CCDS92770, CCDS92771

Canonical transcript exons

ENST00000409933 — 10 exons

ExonStartEnd
ENSE000008101836457948664579546
ENSE000015871086459188864593005
ENSE000034887996457294664573068
ENSE000034969306458542264585545
ENSE000035061306456909264569218
ENSE000035445406456756264567713
ENSE000036141206455144364553409
ENSE000037185306456962364569679
ENSE000039652786458119064581273
ENSE000039656346452432864524612

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 97.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.3247 / max 346.4255, expressed in 1642 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
205893.89631365
205882.0494941
205901.4515511
205920.5042254
205910.4233151

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
renal medullaUBERON:000036297.48gold quality
male germ cellCL:000001597.36gold quality
spermCL:000001997.36gold quality
buccal mucosa cellCL:000233697.29gold quality
cardia of stomachUBERON:000116296.74gold quality
epithelium of nasopharynxUBERON:000195196.67gold quality
cerebellar vermisUBERON:000472096.65gold quality
ileal mucosaUBERON:000033196.59gold quality
type B pancreatic cellCL:000016996.49gold quality
pylorusUBERON:000116696.42gold quality
parotid glandUBERON:000183196.36gold quality
olfactory bulbUBERON:000226496.31silver quality
oviduct epitheliumUBERON:000480496.17gold quality
nasal cavity epitheliumUBERON:000538496.11gold quality
tongue squamous epitheliumUBERON:000691995.85gold quality
nippleUBERON:000203095.79gold quality
superior surface of tongueUBERON:000737195.26gold quality
pharyngeal mucosaUBERON:000035595.13gold quality
upper arm skinUBERON:000426394.98gold quality
diaphragmUBERON:000110394.92silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099194.82gold quality
islet of LangerhansUBERON:000000694.73gold quality
tracheaUBERON:000312694.71gold quality
mucosa of paranasal sinusUBERON:000503094.61gold quality
bronchusUBERON:000218594.59gold quality
mucosa of urinary bladderUBERON:000125994.57gold quality
epithelium of bronchusUBERON:000203194.57gold quality
leukocyteCL:000073894.54gold quality
mononuclear cellCL:000084294.54gold quality
monocyteCL:000057694.52gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

124 targeting AFTPH, 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-3613-3P100.0076.367965
HSA-MIR-4262100.0073.263931
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-186-5P99.9970.833707
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-56899.9869.862084
HSA-MIR-548N99.9871.944170
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-548P99.9872.253784
HSA-MIR-314899.9775.066478
HSA-MIR-60799.9773.625593
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-651-3P99.9473.485177
HSA-MIR-205-3P99.9269.923165
HSA-MIR-362-3P99.9166.381267
HSA-MIR-4753-3P99.9071.033786

Literature-anchored findings (GeneRIF, showing 3)

  • the aftiphilin/p200/gamma-synergin complex facilitates AP-1 function (PMID:15758025)
  • Data show that by recruiting aftiphilin/gamma-synergin in addition to clathrin, AP-1 coordinates formation of Weibel-Palade bodies with their acquisition of a regulated secretory phenotype. (PMID:18815278)
  • Expression profiles and prognostic significance of AFTPH in different tumors. (PMID:33090728)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioaftphaENSDARG00000069249
danio_rerioaftphbENSDARG00000071347
mus_musculusAftphENSMUSG00000049659
rattus_norvegicusAftphENSRNOG00000005411
caenorhabditis_elegansWBGENE00021561

Paralogs (1): CLBA1 (ENSG00000140104)

Protein

Protein identifiers

AftiphilinQ6ULP2 (reviewed: Q6ULP2)

All UniProt accessions (8): A0A0U1RR74, A0A8Q3SI61, A0A8Q3SI81, A0A8Q3SIA4, A0A8Q3WKU6, A0A8Q3WM48, B8ZZI9, Q6ULP2

UniProt curated annotations — full annotation on UniProt →

Function. Component of clathrin-coated vesicles. Component of the aftiphilin/p200/gamma-synergin complex, which plays roles in AP1G1/AP-1-mediated protein trafficking including the trafficking of transferrin from early to recycling endosomes, and the membrane trafficking of furin and the lysosomal enzyme cathepsin D between the trans-Golgi network (TGN) and endosomes.

Subunit / interactions. Self-associates. Interacts with GGA1 (via GAE domain). Interacts with GGA3 (via GAE domain), AP1G1 (via GAE domain) and AP1G2 (via GAE domain). Component of the aftiphilin/p200/gamma-synergin complex, at least composed of AFTPH/aftiphilin, HEATR5B/p200a and SYNRG/gamma-synergin, which plays a role in the AP1G1/AP-1-mediated protein trafficking from early to recycling endosomes. Within the complex interacts with HEATR5B/p200a and SYNRG/gamma-synergin; the interactions are direct. Interacts with AP1G1/AP-1; the interaction is required to recruit AFTPH/aftiphilin to the perinuclear region of the cell. Interacts with CLTCL1/Clathrin.

Subcellular location. Cytoplasm. Perinuclear region. Cytoplasmic vesicle. Clathrin-coated vesicle.

Domain organisation. The WXXF motifs mediate binding of accessory proteins to the ear-domain of AP-1, GGAs and AP-2 through hydrophobic interactions. Selective binding to the GAE domains of AP-1 or to the alpha-ear domain of AP-2 is tuned by the acidic context surrounding the motif and the properties of the second residue of the motif itself.

Miscellaneous. May be due to intron retention.

Isoforms (5)

UniProt IDNamesCanonical?
Q6ULP2-11yes
Q6ULP2-62
Q6ULP2-73
Q6ULP2-84
Q6ULP2-95

RefSeq proteins (10): NP_001002243, NP_001362898, NP_001362899, NP_001362900, NP_001362901, NP_001362902, NP_001381924, NP_001381925, NP_060127, NP_982261* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR029205Clathrin-bdDomain
IPR046359Aftin-likeFamily

Pfam: PF15045

UniProt features (34 total): region of interest 7, short sequence motif 5, sequence conflict 5, compositionally biased region 4, modified residue 4, splice variant 4, sequence variant 3, chain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6ULP2-F146.360.00

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 (4): 151, 395, 518, 617

Mutagenesis-validated functional residues (1):

PositionPhenotype
716–718abolishes the interaction with cltcl1/clathrin.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 172 (showing top): chr2p14, GOCC_TRANS_GOLGI_NETWORK, GOCC_COATED_VESICLE, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, GOCC_GOLGI_ASSOCIATED_VESICLE, GOCC_VESICLE_COAT, MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_UP, GOCC_CLATHRIN_COATED_VESICLE, GOCC_TRANS_GOLGI_NETWORK_TRANSPORT_VESICLE_MEMBRANE, GOCC_GOLGI_ASSOCIATED_VESICLE_MEMBRANE, GOCC_CLATHRIN_COAT, GOCC_CLATHRIN_VESICLE_COAT, MARSON_BOUND_BY_FOXP3_STIMULATED, GOCC_CLATHRIN_COATED_VESICLE_MEMBRANE, GOCC_MEMBRANE_PROTEIN_COMPLEX

GO Biological Process (2): protein transport (GO:0015031), intracellular transport (GO:0046907)

GO Molecular Function (2): clathrin binding (GO:0030276), protein binding (GO:0005515)

GO Cellular Component (9): nucleoplasm (GO:0005654), Golgi apparatus (GO:0005794), cytosol (GO:0005829), AP-1 adaptor complex (GO:0030121), trans-Golgi network membrane (GO:0032588), perinuclear region of cytoplasm (GO:0048471), cytoplasm (GO:0005737), clathrin-coated vesicle (GO:0030136), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
cytoplasm4
transport2
intracellular anatomical structure2
intracellular protein localization1
establishment of protein localization1
cellular localization1
establishment of localization in cell1
protein binding1
binding1
nuclear lumen1
endomembrane system1
intracellular membrane-bounded organelle1
clathrin coat of trans-Golgi network vesicle1
clathrin adaptor complex1
trans-Golgi network1
organelle membrane1
coated vesicle1
intracellular vesicle1

Protein interactions and networks

STRING

726 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
AFTPHSYNRGQ9UMZ2693
AFTPHAP1G2O75843546
AFTPHCPNE1Q99829527
AFTPHSTXBP2Q15833480
AFTPHINAFM1C9JVW0464
AFTPHSERTAD2Q14140406
AFTPHNUDCD1Q96RS6392
AFTPHCAAP1Q9H8G2391
AFTPHTBC1D22BQ9NU19391
AFTPHSCYL2Q6P3W7371
AFTPHHEATR5BQ9P2D3370
AFTPHNTSR1P30989366
AFTPHDCAF5Q96JK2350
AFTPHSFT2D2O95562349
AFTPHFAM216AQ8WUB2348
AFTPHTULP4Q9NRJ4348

IntAct

48 interactions, top by confidence:

ABTypeScore
VAPBFAM83Gpsi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
AP1S2AP1G1psi-mi:“MI:0914”(association)0.670
AP1S2AP1G1psi-mi:“MI:0914”(association)0.660
VAPAFAM83Gpsi-mi:“MI:0914”(association)0.640
CLTBPIK3C2Apsi-mi:“MI:0914”(association)0.530
AFTPHSYNRGpsi-mi:“MI:0915”(physical association)0.500
PEX14AFTPHpsi-mi:“MI:0407”(direct interaction)0.440
AP2B1AFTPHpsi-mi:“MI:0407”(direct interaction)0.440
MAP1LC3BAFTPHpsi-mi:“MI:0407”(direct interaction)0.440
STAT5BAFTPHpsi-mi:“MI:0915”(physical association)0.370
AFTPHreppsi-mi:“MI:0915”(physical association)0.370
UBE3AAFTPHpsi-mi:“MI:0915”(physical association)0.370
CskFRYLpsi-mi:“MI:0914”(association)0.350
AP1S2SLC43A3psi-mi:“MI:0914”(association)0.350
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
VAPAFAM83Gpsi-mi:“MI:0914”(association)0.350
AP1M2AP1G1psi-mi:“MI:0914”(association)0.350
ARHGAP18CLTBpsi-mi:“MI:0914”(association)0.350
CLTACLTBpsi-mi:“MI:0914”(association)0.350
TUBA1BSLAIN2psi-mi:“MI:0914”(association)0.350
TUBB4BTUBA1Bpsi-mi:“MI:0914”(association)0.350

BioGRID (79): AFTPH (Affinity Capture-MS), AFTPH (Affinity Capture-MS), AFTPH (Affinity Capture-MS), AFTPH (Affinity Capture-MS), AFTPH (Affinity Capture-MS), AFTPH (Affinity Capture-MS), AFTPH (Affinity Capture-MS), AFTPH (Affinity Capture-MS), AFTPH (Affinity Capture-MS), AFTPH (Synthetic Lethality), AFTPH (Proximity Label-MS), AFTPH (Affinity Capture-MS), AFTPH (Affinity Capture-MS), AP1G1 (Reconstituted Complex), CLTC (Reconstituted Complex)

ESM2 similar proteins: A0A1B0GTU1, A0P8Z5, A2A870, A4IGN8, B0KYV5, D3ZUI5, F1LR10, O00515, O46385, O75128, O75152, O75410, P0DQW0, P42167, P57016, Q4KLH6, Q5NBX1, Q5RDC1, Q5REG6, Q5SV85, Q5U5Q9, Q5ZIB2, Q5ZJJ1, Q61029, Q62733, Q641Q2, Q6INC4, Q6NZF1, Q6PGL7, Q6ULP2, Q6WKZ4, Q6Y685, Q6ZQ03, Q6ZQ06, Q6ZSR9, Q80WT5, Q80X08, Q86UE4, Q8BJ05, Q8K4L3

Diamond homologs: Q6ULP2, Q80WT5, Q8BHN9, Q17QP7, Q5RJN9, Q96F83

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 42 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
Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters6122.8×2e-10
The role of Nef in HIV-1 replication and disease pathogenesis6122.8×2e-10
Lysosome Vesicle Biogenesis773.7×2e-10
Host Interactions of HIV factors665.0×7e-09
Golgi Associated Vesicle Biogenesis745.2×3e-09
trans-Golgi Network Vesicle Budding540.9×2e-06
Translocation of SLC2A4 (GLUT4) to the plasma membrane629.9×7e-07
MHC class II antigen presentation925.9×1e-09

GO biological processes:

GO termPartnersFoldFDR
synaptic vesicle endocytosis560.0×3e-06
intracellular protein transport1018.0×4e-08
vesicle-mediated transport616.1×8e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance128
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1493 predictions. Top by Δscore:

VariantEffectΔscore
2:64551441:A:Cacceptor_loss1.0000
2:64551442:G:GCacceptor_loss1.0000
2:64551442:GGT:Gacceptor_gain1.0000
2:64567554:T:TAacceptor_gain1.0000
2:64567561:GACA:Gacceptor_gain1.0000
2:64567710:GTGG:Gdonor_gain1.0000
2:64567711:TGG:Tdonor_gain1.0000
2:64567712:GG:Gdonor_gain1.0000
2:64567712:GGG:Gdonor_gain1.0000
2:64567713:GG:Gdonor_gain1.0000
2:64567713:GGT:Gdonor_loss1.0000
2:64567714:G:GCdonor_loss1.0000
2:64567714:G:GGdonor_gain1.0000
2:64567715:T:Gdonor_loss1.0000
2:64569219:G:GGdonor_gain1.0000
2:64569223:GTTT:Gdonor_gain1.0000
2:64569610:A:AGacceptor_gain1.0000
2:64569610:AAC:Aacceptor_gain1.0000
2:64569610:AACGT:Aacceptor_gain1.0000
2:64569611:A:Gacceptor_gain1.0000
2:64569612:C:CAacceptor_gain1.0000
2:64569612:C:Gacceptor_gain1.0000
2:64572944:AG:Aacceptor_gain1.0000
2:64572945:GG:Gacceptor_gain1.0000
2:64572945:GGGT:Gacceptor_gain1.0000
2:64573064:TCCAG:Tdonor_loss1.0000
2:64573065:CCAGG:Cdonor_loss1.0000
2:64573066:CAGG:Cdonor_loss1.0000
2:64573067:AGG:Adonor_loss1.0000
2:64573068:GG:Gdonor_loss1.0000

AlphaMissense

6239 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:64579513:T:AW808R1.000
2:64579513:T:CW808R1.000
2:64579515:G:CW808C1.000
2:64579515:G:TW808C1.000
2:64569156:T:AW718R0.999
2:64569156:T:CW718R0.999
2:64572953:T:CL760S0.999
2:64579507:T:CF806L0.999
2:64579509:T:AF806L0.999
2:64579509:T:GF806L0.999
2:64579529:T:CL813P0.999
2:64591977:T:CL918S0.999
2:64591982:T:CF920L0.999
2:64591983:T:CF920S0.999
2:64591984:C:AF920L0.999
2:64591984:C:GF920L0.999
2:64569158:G:CW718C0.998
2:64569158:G:TW718C0.998
2:64569184:T:CL727P0.998
2:64569187:T:CL728S0.998
2:64569202:T:AI733K0.998
2:64569211:G:CR736P0.998
2:64569660:C:AP751H0.998
2:64569660:C:GP751R0.998
2:64569665:T:GY753D0.998
2:64569669:C:AA754E0.998
2:64569678:T:CL757S0.998
2:64579508:T:CF806S0.998
2:64579508:T:GF806C0.998
2:64579529:T:AL813H0.998

dbSNP variants (sampled 300 via entrez): RS1000019309 (2:64530083 G>C), RS1000053713 (2:64580532 T>A,C), RS1000062885 (2:64560071 C>G), RS1000101717 (2:64525598 T>G), RS1000113001 (2:64526007 A>G), RS1000134198 (2:64534467 CTTATAG>C), RS1000154603 (2:64568457 C>A,T), RS1000156790 (2:64544724 G>A), RS1000162191 (2:64576931 A>C,G), RS1000215924 (2:64541589 T>A), RS1000225395 (2:64566784 A>G), RS1000248676 (2:64541261 G>T), RS1000329305 (2:64562513 C>A,T), RS1000351309 (2:64581713 T>C,G), RS1000382342 (2:64555770 A>G)

Disease associations

OMIM: gene MIM:619628 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST005851_16Delirium1.000000e-06
GCST008836_1Lung adenocarcinoma2.000000e-08
GCST009391_27Metabolite levels3.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0010350cholesteryl ester 22:6 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

42 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Fincreases expression, affects cotreatment, increases methylation2
Arsenic Trioxidedecreases response to substance, increases expression2
Tretinoinincreases expression2
Valproic Acidaffects expression, increases expression2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
FR900359affects phosphorylation1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
bisphenol Aaffects cotreatment, affects methylation, increases methylation1
beta-lapachoneincreases expression1
sodium arsenitedecreases expression, increases abundance1
coumarinincreases phosphorylation1
1-nitropyreneincreases expression1
K 7174increases expression1
abrineincreases expression1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-oldecreases expression1
Resveratroldecreases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, affects methylation, increases methylation1
Arsenicdecreases expression, increases abundance1
Vehicle Emissionsaffects expression, increases abundance1
Benzo(a)pyrenedecreases methylation1
Caffeineaffects phosphorylation1
Cannabidiolincreases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Hydrogen Peroxideaffects expression1
Indomethacinaffects cotreatment, increases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_SB89HAP1 AFTPH (-) 1Cancer cell lineMale
CVCL_SB90HAP1 AFTPH (-) 2Cancer cell lineMale

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): delirium