PHIP

gene
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Also known as ndrpBRWD2RepIDDCAF14FLJ20705

Summary

PHIP (PHIP subunit of CUL4-Ring ligase complex, HGNC:15673) is a protein-coding gene on chromosome 6q14.1, encoding PH-interacting protein (Q8WWQ0). Probable regulator of the insulin and insulin-like growth factor signaling pathways. It is haploinsufficient (ClinGen: sufficient evidence).

This gene encodes a protein that binds to the insulin receptor substrate 1 protein and regulates glucose transporter translocation in skeletal muscle cells. The encoded protein may also regulate growth and survival of pancreatic beta cells. Elevated copy number of this gene may be associated with melanoma severity and the encoded protein may promote melanoma metastasis in human patients.

Source: NCBI Gene 55023 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome (Definitive, ClinGen) — +5 more curated relationships
  • GWAS associations: 35
  • Clinical variants (ClinVar): 1,222 total — 55 pathogenic, 67 likely-pathogenic
  • Phenotypes (HPO): 150
  • Druggable target: yes
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_017934

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:15673
Approved symbolPHIP
NamePHIP subunit of CUL4-Ring ligase complex
Location6q14.1
Locus typegene with protein product
StatusApproved
Aliasesndrp, BRWD2, RepID, DCAF14, FLJ20705
Ensembl geneENSG00000146247
Ensembl biotypeprotein_coding
OMIM612870
Entrez55023

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 10 protein_coding, 4 retained_intron, 3 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined

ENST00000275034, ENST00000479165, ENST00000700012, ENST00000700013, ENST00000700114, ENST00000700115, ENST00000700116, ENST00000700117, ENST00000700118, ENST00000700119, ENST00000700120, ENST00000700121, ENST00000700170, ENST00000700171, ENST00000700172, ENST00000913657, ENST00000913658, ENST00000913659, ENST00000913660, ENST00000965196

RefSeq mRNA: 1 — MANE Select: NM_017934 NM_017934

CCDS: CCDS4987

Canonical transcript exons

ENST00000275034 — 40 exons

ExonStartEnd
ENSE000018825657907802979078254
ENSE000022039537907744879077507
ENSE000022153177902551979025619
ENSE000022166017895847578958600
ENSE000022212057901654479016642
ENSE000022238947898288678983117
ENSE000022338437907770079077729
ENSE000022402067901563079015783
ENSE000022429897900373079003858
ENSE000022564787901508279015216
ENSE000022607247900189979002124
ENSE000022686567902594379026164
ENSE000022715317898820978988349
ENSE000022747647906047879060576
ENSE000022766487899741478997597
ENSE000022799057901748379017583
ENSE000022836157899825478998391
ENSE000022842157898535278985428
ENSE000022918837904284379043003
ENSE000023053297906066879060818
ENSE000023061527901734679017386
ENSE000023135967901908979019159
ENSE000023167347907785579077913
ENSE000023206847899086878990985
ENSE000024884517895561378955682
ENSE000035020727894600178946260
ENSE000035056617897078178970888
ENSE000035386887897004978970173
ENSE000035460517894530078945497
ENSE000035480377897859278978711
ENSE000035480737896169078961810
ENSE000035563267895523278955282
ENSE000035766517893441978941330
ENSE000035786447896309778963252
ENSE000036094797894762378947775
ENSE000036108927896570378965764
ENSE000036176037894671178946874
ENSE000036269187896983578969917
ENSE000036314747896594578966056
ENSE000036561047895481478954963

Expression profiles

Bgee: expression breadth ubiquitous, 302 present calls, max score 97.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 37.0593 / max 664.6102, expressed in 1819 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
7450026.57141807
745017.48991684
744981.8877755
744991.1104487

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bronchial epithelial cellCL:000232897.67gold quality
epithelium of bronchusUBERON:000203197.37gold quality
ventricular zoneUBERON:000305397.35gold quality
bronchusUBERON:000218597.27gold quality
endothelial cellCL:000011596.90gold quality
cerebellar vermisUBERON:000472096.74gold quality
mucosa of paranasal sinusUBERON:000503096.15gold quality
pigmented layer of retinaUBERON:000178295.90gold quality
retinaUBERON:000096695.87gold quality
mammary ductUBERON:000176595.80gold quality
trabecular bone tissueUBERON:000248395.80gold quality
choroid plexus epitheliumUBERON:000391195.73gold quality
epithelium of nasopharynxUBERON:000195195.62gold quality
pericardiumUBERON:000240795.61gold quality
nasopharynxUBERON:000172895.60gold quality
epithelium of mammary glandUBERON:000324495.58gold quality
cranial nerve IIUBERON:000094195.48gold quality
hair follicleUBERON:000207395.05gold quality
superficial temporal arteryUBERON:000161494.93gold quality
urethraUBERON:000005794.88gold quality
seminal vesicleUBERON:000099894.75gold quality
oviduct epitheliumUBERON:000480494.71gold quality
calcaneal tendonUBERON:000370194.63gold quality
embryoUBERON:000092294.15gold quality
upper leg skinUBERON:000426294.08gold quality
lower lobe of lungUBERON:000894993.94gold quality
cardia of stomachUBERON:000116293.85gold quality
CA1 field of hippocampusUBERON:000388193.85gold quality
cauda epididymisUBERON:000436093.83gold quality
caput epididymisUBERON:000435893.81gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-HCAD-5yes42.57
E-ANND-3yes10.46
E-GEOD-75140no1396.37
E-MTAB-6524no274.82

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

481 targeting PHIP, 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-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3163100.0077.238605
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5692A100.0074.406850
HSA-MIR-3924100.0072.092394
HSA-MIR-3646100.0073.565283
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4262100.0073.263931
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-8485100.0077.574731
HSA-MIR-340-5P100.0072.504437
HSA-MIR-9-5P100.0072.282361
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-6833-3P100.0070.633197

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 11)

  • The PHIP gene resides on 6q14.1, and although 6q loss has been observed in melanoma, the PHIP locus was preserved in melanoma cell lines and patient samples, and its overexpression was an independent adverse predictor of survival in melanoma patients. (PMID:22511720)
  • These results provide further support for PHIP as a molecular prognostic marker of melanoma, and reveal a significant linkage between PHIP levels and ulceration. (PMID:24005052)
  • as elevated PHIP copy number appears to be selected for during the progression of primary to metastatic melanoma, these results confirm PHIP as a promising therapeutic target for melanoma. (PMID:29776954)
  • The replication initiation determinant protein PHIP modulates replication by recruiting CUL4 to chromatin. (PMID:30018425)
  • During mitosis, CRL4 dissociates from RepID and replaces it with RB Binding Protein 7 (RBBP7), which ubiquitinates the SAC mediator BUB3 to enable mitotic exit. (PMID:31911655)
  • PHIP drives glioblastoma motility, invasion, and angiogenesis. PHIP regulates expression of focal adhesion proteins and physically interacts with vinculin, mechanisms by which it promotes tumor cell motility and invasion. The presence of elevated PHIP copy number in distinct molecular glioblastoma subtypes provides additional support for its importance to glioblastoma biology. (PMID:32273388)
  • Exome Sequencing Identifies Genes and Gene Sets Contributing to Severe Childhood Obesity, Linking PHIP Variants to Repressed POMC Transcription. (PMID:32492392)
  • Discovery of a hidden transient state in all bromodomain families. (PMID:33468647)
  • DCAF14 promotes stalled fork stability to maintain genome integrity. (PMID:33503431)
  • Molecular double clips within RepID WD40 domain control chromatin binding and CRL4-substrate assembly. (PMID:34171797)
  • A trivalent nucleosome interaction by PHIP/BRWD2 is disrupted in neurodevelopmental disorders and cancer. (PMID:34819353)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriophipENSDARG00000015970
mus_musculusPhipENSMUSG00000032253
rattus_norvegicusPhipENSRNOG00000008652
drosophila_melanogasterBRWD3FBGN0011785

Paralogs (2): BRWD3 (ENSG00000165288), BRWD1 (ENSG00000185658)

Protein

Protein identifiers

PH-interacting proteinQ8WWQ0 (reviewed: Q8WWQ0)

Alternative names: DDB1- and CUL4-associated factor 14, IRS-1 PH domain-binding protein, WD repeat-containing protein 11

All UniProt accessions (8): Q8WWQ0, A0A8V8TP75, A0A8V8TPB8, A0A8V8TPK0, A0A8V8TPV5, A0A8V8TQM4, A0A8V8TQP5, A0A8V8TQZ3

UniProt curated annotations — full annotation on UniProt →

Function. Probable regulator of the insulin and insulin-like growth factor signaling pathways. Stimulates cell proliferation through regulation of cyclin transcription and has an anti-apoptotic activity through AKT1 phosphorylation and activation. Plays a role in the regulation of cell morphology and cytoskeletal organization.

Subunit / interactions. Interacts with IRS1 and IRS2. Interacts (via bromo domain) with acetylated lysine residues on histone H1.4, histone H3 and H4 (in vitro).

Subcellular location. Nucleus.

Tissue specificity. Expressed in myeloma and epidermoid carcinoma cell lines.

Disease relevance. Chung-Jansen syndrome (CHUJANS) [MIM:617991] An autosomal dominant disorder characterized by developmental delay, intellectual disability, autistic features, anxiety, hypotonia, obesity, and dysmorphic features. The disease is caused by variants affecting the gene represented in this entry.

RefSeq proteins (1): NP_060404* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001487BromodomainDomain
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR018359Bromodomain_CSConserved_site
IPR019775WD40_repeat_CSConserved_site
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR036427Bromodomain-like_sfHomologous_superfamily
IPR052060Bromo_WD_repeatFamily
IPR057451BRWD/PHIP_ADDomain
IPR057452BRWD/PHIP_NDomain

Pfam: PF00400, PF00439, PF25313, PF25437

UniProt features (92 total): modified residue 25, sequence variant 19, compositionally biased region 11, repeat 8, region of interest 8, helix 6, cross-link 5, sequence conflict 3, turn 3, domain 2, chain 1, strand 1

Structure

Experimental structures (PDB)

146 structures, top 30 by resolution.

PDBMethodResolution (Å)
5S9GX-RAY DIFFRACTION1.09
5S90X-RAY DIFFRACTION1.1
5S98X-RAY DIFFRACTION1.1
5S9CX-RAY DIFFRACTION1.14
5S8XX-RAY DIFFRACTION1.15
5S97X-RAY DIFFRACTION1.15
5S9JX-RAY DIFFRACTION1.15
7FUSX-RAY DIFFRACTION1.15
7FUYX-RAY DIFFRACTION1.15
7FV2X-RAY DIFFRACTION1.15
7FV3X-RAY DIFFRACTION1.15
7FV4X-RAY DIFFRACTION1.15
7FV5X-RAY DIFFRACTION1.15
7FV8X-RAY DIFFRACTION1.15
7FVFX-RAY DIFFRACTION1.15
7FVGX-RAY DIFFRACTION1.15
7FVHX-RAY DIFFRACTION1.15
7FVKX-RAY DIFFRACTION1.15
7FVLX-RAY DIFFRACTION1.15
7FVNX-RAY DIFFRACTION1.15
7FVPX-RAY DIFFRACTION1.15
7FVQX-RAY DIFFRACTION1.15
5RJJX-RAY DIFFRACTION1.15
5S9BX-RAY DIFFRACTION1.15
7FUUX-RAY DIFFRACTION1.16
5RJTX-RAY DIFFRACTION1.17
5S96X-RAY DIFFRACTION1.17
7FV9X-RAY DIFFRACTION1.17
5S8FX-RAY DIFFRACTION1.18
5S8VX-RAY DIFFRACTION1.18

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8WWQ0-F166.570.32

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 (30): 136, 641, 659, 674, 677, 683, 692, 879, 880, 881, 911, 1281, 1283, 1296, 1315, 1359, 1405, 1479, 1497, 1525 …

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-9013418RHOBTB2 GTPase cycle

MSigDB gene sets: 866 (showing top): GOBP_DNA_TEMPLATED_DNA_REPLICATION_MAINTENANCE_OF_FIDELITY, GOBP_POSITIVE_REGULATION_OF_MITOTIC_NUCLEAR_DIVISION, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_REGULATION_OF_PHOSPHORYLATION, GOBP_VESICLE_LOCALIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_REGULATION_OF_NUCLEAR_DIVISION, MODULE_255, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOCC_VACUOLAR_MEMBRANE, MORF_SNRP70, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP

GO Biological Process (15): regulation of protein phosphorylation (GO:0001932), regulation of transcription by RNA polymerase II (GO:0006357), cytoskeleton organization (GO:0007010), positive regulation of cell population proliferation (GO:0008284), insulin receptor signaling pathway (GO:0008286), regulation of cell shape (GO:0008360), regulation of cell morphogenesis (GO:0022604), negative regulation of apoptotic process (GO:0043066), positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568), positive regulation of mitotic nuclear division (GO:0045840), positive regulation of DNA-templated transcription (GO:0045893), positive regulation of transcription by RNA polymerase II (GO:0045944), negative regulation of extrinsic apoptotic signaling pathway (GO:2001237), chromatin organization (GO:0006325), regulation of signal transduction (GO:0009966)

GO Molecular Function (3): insulin receptor binding (GO:0005158), histone reader activity (GO:0140566), protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
RHOBTB GTPase Cycle1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription2
transcription by RNA polymerase II2
protein phosphorylation1
regulation of protein modification process1
regulation of phosphorylation1
organelle organization1
cell population proliferation1
regulation of cell population proliferation1
positive regulation of cellular process1
cell surface receptor protein tyrosine kinase signaling pathway1
cellular response to insulin stimulus1
regulation of cell morphogenesis1
regulation of biological quality1
cell morphogenesis1
regulation of anatomical structure morphogenesis1
apoptotic process1
regulation of apoptotic process1
negative regulation of programmed cell death1
positive regulation of signal transduction1
regulation of insulin-like growth factor receptor signaling pathway1
insulin-like growth factor receptor signaling pathway1
regulation of mitotic nuclear division1
positive regulation of nuclear division1
positive regulation of cell cycle process1
mitotic nuclear division1
DNA-templated transcription1
positive regulation of RNA biosynthetic process1
regulation of transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
extrinsic apoptotic signaling pathway1
negative regulation of apoptotic signaling pathway1
regulation of extrinsic apoptotic signaling pathway1
cellular component organization1
signal transduction1
regulation of cell communication1
regulation of signaling1
regulation of response to stimulus1
signaling receptor binding1
nucleosome1
histone binding1

Protein interactions and networks

STRING

2612 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PHIPIRAK1BP1Q5VVH5575
PHIPSPATA25Q9BR10504
PHIPIRS2Q9Y4H2497
PHIPLRWD1Q9UFC0422
PHIPCUL4BQ13620392
PHIPACSS3Q9H6R3383
PHIPZMYM4Q5VZL5378
PHIPDDB1Q16531373
PHIPGLT8D1Q68CQ7367
PHIPMTCL2O94964360
PHIPSCYL2Q6P3W7360
PHIPACOT8O14734354
PHIPCRLS1Q9UJA2341
PHIPPLEKHF2Q9H8W4335
PHIPSMARCA4P51532334

IntAct

51 interactions, top by confidence:

ABTypeScore
CUL4ACOPS2psi-mi:“MI:0914”(association)0.640
VHLPHIPpsi-mi:“MI:0915”(physical association)0.560
H3C1SMCHD1psi-mi:“MI:2364”(proximity)0.410
PHIPHNRNPCL2psi-mi:“MI:0915”(physical association)0.400
PHIPTPRpsi-mi:“MI:0915”(physical association)0.400
PHIPLMNApsi-mi:“MI:0915”(physical association)0.400
PHIPHSPA5psi-mi:“MI:0915”(physical association)0.400
Cbx1psi-mi:“MI:0914”(association)0.350
Chaf1aCBX5psi-mi:“MI:0914”(association)0.350
RPL10RPS6psi-mi:“MI:0914”(association)0.350
AtrxELOCpsi-mi:“MI:0914”(association)0.350
Brwd3WDR91psi-mi:“MI:0914”(association)0.350
CUL4BGPS1psi-mi:“MI:0914”(association)0.350
Cul4aGPS1psi-mi:“MI:0914”(association)0.350
MPHOSPH8HCFC1psi-mi:“MI:0914”(association)0.350
TMPOpsi-mi:“MI:0914”(association)0.350
EGR1MAGEB2psi-mi:“MI:0914”(association)0.350
Eif3eRPSApsi-mi:“MI:0914”(association)0.350
ORC1ZNF768psi-mi:“MI:0914”(association)0.350
CUL4AHAX1psi-mi:“MI:0914”(association)0.350
DCUN1D1RGSL1psi-mi:“MI:0914”(association)0.350
CUL4BAPBB1psi-mi:“MI:0914”(association)0.350
DCUN1D1KLHL18psi-mi:“MI:0914”(association)0.350
CACNA1CSNRPGP15psi-mi:“MI:0914”(association)0.350
TXNIPZSWIM8psi-mi:“MI:0914”(association)0.350
H2BC21SMCHD1psi-mi:“MI:0914”(association)0.350
HMGA1SUPT5Hpsi-mi:“MI:0914”(association)0.350
HMGN5SMCHD1psi-mi:“MI:0914”(association)0.350

BioGRID (394): CUL4B (Affinity Capture-Western), CUL4A (Affinity Capture-Western), DDB1 (Affinity Capture-Western), PHIP (Affinity Capture-MS), PHIP (Affinity Capture-MS), PHIP (Affinity Capture-MS), DDB1 (Co-fractionation), PHIP (Affinity Capture-MS), PHIP (Proximity Label-MS), PHIP (Proximity Label-MS), PHIP (Proximity Label-MS), PHIP (Affinity Capture-MS), PHIP (Affinity Capture-MS), PHIP (Affinity Capture-MS), PHIP (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IES7, A0JN62, A0JNW5, A2AAE1, A2AGL3, A2RSJ4, A2RT67, A2RUS2, A2RV80, B0LPN4, B1H2P5, E7F240, E9Q401, O00507, O94967, P30957, P48553, P51593, Q14161, Q2LD37, Q3TLI0, Q3UHE1, Q3UVG3, Q3UX43, Q5F361, Q5M7Q1, Q5RAQ5, Q5ZJK1, Q658Y4, Q68CL5, Q6BDS2, Q6P6Y1, Q6TEP1, Q6VNB8, Q7TMY8, Q7TSG1, Q7Z6Z7, Q8BHY8, Q8CB44, Q8CGF6

Diamond homologs: A0A0R4IXF6, A0A7U2QYM2, A2AHJ4, A2AUY4, A2BIL7, B2RRD7, B7ZS37, D4A7T3, E9Q2Z1, F1QW93, F1R5H6, F7DRV9, G5E8P1, O15164, O60885, O74350, O88379, O88665, O95696, P13709, P21675, P25440, P35817, P51123, P53236, P54816, P55201, P87152, Q02206, Q03330, Q07442, Q08D75, Q09948, Q12830, Q15059, Q1LUC3, Q23590, Q32S26, Q338B9, Q4R8Y1

SIGNOR signaling

2 interactions.

AEffectBMechanism
PHIP“up-regulates activity”Cullin4-RBX1-DDB1binding
PHIP“up-regulates activity”IRS1binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 74 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
Regulation of expression of SLITs and ROBOs68.3×8e-03
Neddylation76.6×8e-03

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation514.7×4e-03
chromatin organization69.4×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

1222 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic55
Likely pathogenic67
Uncertain significance498
Likely benign336
Benign192

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1073105NM_017934.7(PHIP):c.1050dup (p.Gly351fs)Pathogenic
1098849NM_018117.12(WDR11):c.1255C>T (p.Gln419Ter)Pathogenic
1098850NM_018117.12(WDR11):c.2931+1G>APathogenic
1098851NM_018117.12(WDR11):c.1439del (p.Asn480fs)Pathogenic
1424195NC_000006.11:g.(?79650410)(79787785_?)delPathogenic
1676029NM_017934.7(PHIP):c.2668C>T (p.Gln890Ter)Pathogenic
1686056NM_017934.7(PHIP):c.2703dup (p.Val902fs)Pathogenic
1698953NM_017934.7(PHIP):c.704_705del (p.Asn234_Tyr235insTer)Pathogenic
1708636NM_017934.7(PHIP):c.748C>T (p.Arg250Ter)Pathogenic
1710707NM_017934.7(PHIP):c.241C>T (p.Arg81Ter)Pathogenic
1711633NM_017934.7(PHIP):c.1628_1653+13delPathogenic
1722952NM_017934.7(PHIP):c.2656G>T (p.Glu886Ter)Pathogenic
2067762NM_018117.12(WDR11):c.1280T>G (p.Leu427Ter)Pathogenic
2103265NM_018117.12(WDR11):c.1153del (p.Leu385fs)Pathogenic
2227896NM_017934.7(PHIP):c.2363del (p.Lys788fs)Pathogenic
2499020NM_017934.7(PHIP):c.2537+2T>APathogenic
2571255NM_017934.7(PHIP):c.703del (p.Tyr235fs)Pathogenic
2630755NM_017934.7(PHIP):c.2670_2671del (p.Lys891fs)Pathogenic
2664240NM_017934.7(PHIP):c.1654-2A>CPathogenic
2664242NM_017934.7(PHIP):c.2306_2309del (p.Pro769fs)Pathogenic
2664253NM_017934.7(PHIP):c.820C>T (p.Gln274Ter)Pathogenic
2762988NM_017934.7(PHIP):c.815C>G (p.Ser272Ter)Pathogenic
2785929NM_017934.7(PHIP):c.1446_1447del (p.Ser484fs)Pathogenic
3027385NM_017934.7(PHIP):c.1949_1950delinsGTTG (p.Leu650fs)Pathogenic
3239498NM_017934.7(PHIP):c.857dup (p.Ser287fs)Pathogenic
3359039NM_017934.7(PHIP):c.1879+1G>APathogenic
3372383NM_017934.7(PHIP):c.97C>T (p.Gln33Ter)Pathogenic
3638700NM_017934.7(PHIP):c.368dup (p.Ala124fs)Pathogenic
3653303NM_017934.7(PHIP):c.1300C>T (p.Arg434Ter)Pathogenic
3764548NM_017934.7(PHIP):c.2246dup (p.Thr750fs)Pathogenic

SpliceAI

6172 predictions. Top by Δscore:

VariantEffectΔscore
6:78945295:CTTAC:Cdonor_loss1.0000
6:78945297:TAC:Tdonor_loss1.0000
6:78945298:A:Cdonor_loss1.0000
6:78945299:C:Gdonor_loss1.0000
6:78945299:CCTTG:Cdonor_gain1.0000
6:78945495:GTA:Gacceptor_gain1.0000
6:78945498:C:CCacceptor_gain1.0000
6:78945505:A:Cacceptor_gain1.0000
6:78945994:GTCTT:Gdonor_loss1.0000
6:78945998:TACT:Tdonor_loss1.0000
6:78945999:A:ACdonor_gain1.0000
6:78946000:C:Adonor_loss1.0000
6:78946000:C:CCdonor_gain1.0000
6:78946000:CTT:Cdonor_gain1.0000
6:78946008:C:Adonor_gain1.0000
6:78946256:CAGGG:Cacceptor_gain1.0000
6:78946257:AGGG:Aacceptor_gain1.0000
6:78946258:GGG:Gacceptor_gain1.0000
6:78946258:GGGC:Gacceptor_loss1.0000
6:78946259:GG:Gacceptor_gain1.0000
6:78946259:GGC:Gacceptor_loss1.0000
6:78946260:GC:Gacceptor_loss1.0000
6:78946261:C:CCacceptor_gain1.0000
6:78946723:C:CTdonor_gain1.0000
6:78946724:T:TTdonor_gain1.0000
6:78946870:TAAAT:Tacceptor_gain1.0000
6:78946872:AAT:Aacceptor_gain1.0000
6:78946875:C:CCacceptor_gain1.0000
6:78946875:CT:Cacceptor_loss1.0000
6:78947619:ATAC:Adonor_gain1.0000

AlphaMissense

11990 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:78946852:A:GL1410P1.000
6:78947646:A:CY1395D1.000
6:78947656:A:CN1391K1.000
6:78947656:A:TN1391K1.000
6:78947669:A:GL1387P1.000
6:78947732:A:TV1366D1.000
6:78947772:A:GY1353H1.000
6:78954845:A:GF1341S1.000
6:78954906:A:GW1321R1.000
6:78954906:A:TW1321R1.000
6:78958543:A:CF1238L1.000
6:78958543:A:TF1238L1.000
6:78958545:A:GF1238L1.000
6:78958581:A:GW1226R1.000
6:78958581:A:TW1226R1.000
6:78965730:A:GW1118R1.000
6:78965730:A:TW1118R1.000
6:78965734:A:CS1116R1.000
6:78965734:A:TS1116R1.000
6:78965736:T:GS1116R1.000
6:78965761:C:AW1107C1.000
6:78965761:C:GW1107C1.000
6:78965762:C:GW1107S1.000
6:78965763:A:GW1107R1.000
6:78965763:A:TW1107R1.000
6:78965948:A:TV1105D1.000
6:78966014:C:AG1083V1.000
6:78966014:C:TG1083E1.000
6:78966015:C:GG1083R1.000
6:78966015:C:TG1083R1.000

dbSNP variants (sampled 300 via entrez): RS1000011484 (6:78989571 A>G), RS1000038125 (6:79051215 T>C), RS1000043880 (6:79078248 A>G), RS1000044372 (6:78940322 C>T), RS1000047406 (6:78969755 C>A,G), RS1000094732 (6:79076246 G>A), RS1000104981 (6:78995134 C>T), RS1000114851 (6:79002655 T>C,G), RS1000117673 (6:78942094 T>C), RS1000129041 (6:78993298 C>T), RS1000153775 (6:79046451 C>G,T), RS1000163261 (6:79030544 G>C), RS1000177442 (6:78963688 A>G), RS1000185367 (6:79002304 T>G), RS1000227296 (6:78996678 A>G)

Disease associations

OMIM: gene MIM:612870 | disease phenotypes: MIM:617991, MIM:620237, MIM:614858, MIM:146110, MIM:300958, MIM:147950, MIM:616839

GenCC curated gene-disease

DiseaseClassificationInheritance
developmental delay, intellectual disability, obesity, and dysmorphic featuresDefinitiveAutosomal dominant
PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndromeDefinitiveAutosomal dominant
hypogonadotropic hypogonadism 14 with or without anosmiaStrongAutosomal dominant
intellectual developmental disorder, autosomal recessive 78StrongAutosomal recessive
hypogonadotropic hypogonadismSupportiveAutosomal dominant
Kallmann syndromeSupportiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndromeDefinitiveAD

Mondo (15): PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome (MONDO:0035133), microcephaly (MONDO:0001149), intellectual developmental disorder, autosomal recessive 78 (MONDO:0859373), hypogonadotropic hypogonadism 14 with or without anosmia (MONDO:0013926), hypogonadotropic hypogonadism 7 with or without anosmia (MONDO:0007794), amenorrhea (MONDO:0001836), intellectual disability, X-linked 102 (MONDO:0010497), autism spectrum disorder (MONDO:0005258), hypogonadotropic hypogonadism (MONDO:0018555), intellectual disability (MONDO:0001071), exercise intolerance, riboflavin-responsive (MONDO:0014795), CHARGE syndrome (MONDO:0008965), hereditary breast ovarian cancer syndrome (MONDO:0003582), (MONDO:0060712), Kallmann syndrome (MONDO:0018800)

Orphanet (8): PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome (Orphanet:589905), Kallmann syndrome (Orphanet:478), Normosmic congenital hypogonadotropic hypogonadism (Orphanet:432), X-linked intellectual disability-hypotonia-movement disorder syndrome (Orphanet:457260), CHARGE syndrome (Orphanet:138), Hereditary breast and/or ovarian cancer syndrome (Orphanet:145), NON RARE IN EUROPE: Autism (Orphanet:106), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

150 total (30 of 150 shown, HPO-id order):

HPOTerm
HP:0000002Abnormality of body height
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000008Abnormal morphology of female internal genitalia
HP:0000013Hypoplasia of the uterus
HP:0000026Male hypogonadism
HP:0000027Azoospermia
HP:0000028Cryptorchidism
HP:0000044Hypogonadotropic hypogonadism
HP:0000054Micropenis
HP:0000104Renal agenesis
HP:0000118Phenotypic abnormality
HP:0000134Female hypogonadism
HP:0000144Decreased fertility
HP:0000164Abnormality of the dentition
HP:0000175Cleft palate
HP:0000218High palate
HP:0000233Thin vermilion border
HP:0000252Microcephaly
HP:0000278Retrognathia
HP:0000286Epicanthus
HP:0000308Microretrognathia
HP:0000311Round face
HP:0000316Hypertelorism
HP:0000322Short philtrum
HP:0000343Long philtrum
HP:0000347Micrognathia
HP:0000348High forehead
HP:0000400Macrotia
HP:0000403Recurrent otitis media

GWAS associations

35 associations (top):

StudyTraitp-value
GCST001525_23Visceral fat6.000000e-06
GCST001762_862Obesity-related traits5.000000e-06
GCST002233_1Adiponectin levels3.000000e-14
GCST002976_5HIV-1 viral setpoint6.000000e-06
GCST004093_13Prostate-specific antigen levels3.000000e-11
GCST004093_14Prostate-specific antigen levels4.000000e-18
GCST004093_15Prostate-specific antigen levels1.000000e-35
GCST004093_16Prostate-specific antigen levels4.000000e-43
GCST004094_1Prostate-specific antigen levels (conditioned on lead SNPs)9.000000e-25
GCST004094_7Prostate-specific antigen levels (conditioned on lead SNPs)5.000000e-18
GCST004879_3Sjögren’s syndrome6.000000e-06
GCST005316_564Intelligence (MTAG)6.000000e-10
GCST005316_565Intelligence (MTAG)6.000000e-10
GCST006227_5Diastolic blood pressure3.000000e-09
GCST006231_30Mean arterial pressure2.000000e-06
GCST007094_26Diastolic blood pressure2.000000e-13
GCST007099_78Systolic blood pressure4.000000e-09
GCST007267_218Systolic blood pressure8.000000e-12
GCST007507_14Benign prostatic hyperplasia and lower urinary tract symptoms3.000000e-15
GCST007513_2Prostate-specific antigen levels7.000000e-08
GCST007847_101Type 2 diabetes3.000000e-09
GCST007847_54Type 2 diabetes5.000000e-08
GCST008860_8Prostate cancer8.000000e-06
GCST009380_3Type 2 diabetes (adjusted for BMI)4.000000e-09
GCST009391_1160Metabolite levels1.000000e-06
GCST009391_282Metabolite levels2.000000e-06
GCST009391_291Metabolite levels2.000000e-06
GCST009391_367Metabolite levels4.000000e-06
GCST009614_2LDL cholesterol levels x loop diuretics use interaction4.000000e-08
GCST010118_118Type 2 diabetes5.000000e-17

EFO canonical traits (16, from GWAS)

EFO IDTrait name
EFO:0003939energy intake
EFO:0004502adiponectin measurement
EFO:0006319HIV viral set point measurement
EFO:0004337intelligence
EFO:0006336diastolic blood pressure
EFO:0006340mean arterial pressure
EFO:0006335systolic blood pressure
EFO:0008008lower urinary tract symptom
EFO:0010460anthranilic acid measurement
EFO:0010424triacylglycerol 54:6 measurement
EFO:0010425triacylglycerol 54:7 measurement
EFO:0010435triacylglycerol 56:8 measurement
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004614apolipoprotein A 1 measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0011013vaginal microbiome measurement

MeSH disease descriptors (7)

DescriptorNameTree numbers
D000568AmenorrheaC23.550.568.500
D058747CHARGE SyndromeC09.218.458.341.186.500.250; C10.597.751.418.341.186.500.250; C10.597.751.941.162.625.250; C11.270.147.500; C11.966.075.375.250; C16.131.077.299.250; C16.320.165; C23.888.592.763.393.341.186.500.500; C23.888.592.763.941.162.625.500
D061325Hereditary Breast and Ovarian Cancer SyndromeC04.588.180.483; C04.588.322.455.431; C04.700.517; C12.050.351.500.056.630.705.431; C12.050.351.937.418.685.431; C12.100.250.056.630.705.431; C12.900.418.685.431; C16.320.700.517; C17.800.090.500.483; C19.344.410.431; C19.391.630.705.431
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D017436Kallmann SyndromeC12.050.351.875.253.096.750; C12.200.706.316.096.750; C12.800.316.096.750; C16.131.939.316.096.750; C16.320.467; C19.391.119.096.750; C19.391.482.600
D008831MicrocephalyC05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500
C562785Idiopathic Hypogonadotropic Hypogonadism (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2176773 (SINGLE PROTEIN)

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: other protein — Non-enzymatic BRD containing proteins

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects methylation, decreases expression, increases abundance, increases expression4
Valproic Acidaffects cotreatment, decreases expression4
trichostatin Aaffects expression, decreases expression2
Panobinostataffects cotreatment, decreases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
TAK-243decreases sumoylation1
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
sodium arsenatedecreases expression1
decabromobiphenyl etherdecreases expression1
arseniteaffects binding, decreases reaction1
tetrabromobisphenol Adecreases expression1
manganese chloridedecreases expression, increases abundance1
potassium chromate(VI)affects cotreatment, decreases expression1
coumarinincreases phosphorylation1
beta-methylcholineaffects expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608increases reaction, affects binding1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
bisphenol Saffects expression1
jinfukangdecreases expression1
Resveratrolaffects cotreatment, increases expression1
Arsenicdecreases expression, increases abundance1

ChEMBL screening assays

17 unique, capped per target: 17 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL2186998BindingInhibition of His6FLAG-tagged PHIP-BD2 expressed in Escherichia coli assessed as change in melting temperature at 100 uM by thermal shift assayFragment-based discovery of bromodomain inhibitors part 2: optimization of phenylisoxazole sulfonamides. — J Med Chem

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B2ALAbcam HeLa PHIP KOCancer cell lineFemale
CVCL_TD25HAP1 PHIP (-) 1Cancer cell lineMale
CVCL_TD26HAP1 PHIP (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00328926PHASE4TERMINATEDLuveris® (Lutropin Alfa for Injection) in Women With Hypogonadotropic Hypogonadism (Luteinizing Hormone [LH] Less Than [<] 1.2 International Unit Per Liter [IU/L])
NCT01403532PHASE4COMPLETEDSequential Therapy for Hypogonadotropic Hypogonadism
NCT01454011PHASE4COMPLETEDThe Effect of Testosterone Replacement on the High Density Lipoprotein Cholesterol Subgroups
NCT01601327PHASE4COMPLETEDEffects of Medications in Patients With Hypogonadism
NCT02310074PHASE4UNKNOWNEfficacy and Safety of Pulsatile Gonadotropin Releasing Hormone Pump Treatment in Patients With Idiopathic Hypogonadotropic Hypogonadism
NCT02880280PHASE4UNKNOWNHuman Menopausal Gonadotropin Combining With Human Chorionic Gonadotropin Treat Congenital Hypogonadotropic Hypogonadism
NCT03490513PHASE4COMPLETEDAromatase Inhibitors and Weight Loss in Severely Obese Men With Hypogonadism
NCT04456296PHASE4COMPLETEDA Study of the Effect of Testosterone Replacement Therapy on Blood Pressure in Adult Male Participants With Hypogonadism
NCT05205837PHASE4TERMINATEDA Randomized, Double-blinded, Clinical, Placebo-controlled Trial on the Effects of Therapy With Letrozole and hUman Choriongonadotropin in Male Hypogonadism Induced by Illicit Use of Anabolic Androgenic Steroids- The LUCAS Trial
NCT03687606PHASE4UNKNOWNEfficacy and Safety of Long Term Use of hCG or hCG Plus hMG in Males With Isolated Hypogonadotropic Hypogonadism (IHH)
NCT01103518PHASE4UNKNOWNEthinyl Estradiol and Cyproterone Acetate in Irregular Menstruation
NCT01206153PHASE4COMPLETEDMetformin for Treatment Antipsychotic Induced Amenorrhea in Female Schizophrenic Patients
NCT02393482PHASE4UNKNOWNPsychological Impact of Amenorrhea in Women With Endometriosis
NCT00391261PHASE4COMPLETEDAn Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820PHASE4COMPLETEDFMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01333865PHASE4COMPLETEDA Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700PHASE4COMPLETEDMilnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200PHASE4COMPLETEDOmega-3 Fatty Acids in Autism Spectrum Disorders
NCT02096952PHASE4COMPLETEDMethylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02235467PHASE4COMPLETEDMultisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02940574PHASE4COMPLETEDNeural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629PHASE4COMPLETEDPromoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646PHASE4COMPLETEDEvaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431PHASE4COMPLETEDImproving Driving in Young People With Autism Spectrum Disorders
NCT03757585PHASE4COMPLETEDNatural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353PHASE4COMPLETEDPragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656PHASE4COMPLETEDBiomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245PHASE4UNKNOWNSafety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339PHASE4RECRUITINGAWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052PHASE4TERMINATEDA Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665PHASE4RECRUITINGThe TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697PHASE4COMPLETEDPilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804PHASE4COMPLETEDPilot RCT Using Homeopathic Medicines in ASD
NCT07439042PHASE4NOT_YET_RECRUITINGBuspirone for Anxiety in Autistic Youth
NCT00467870PHASE3COMPLETEDLong-term Safety Study of Intramuscular Injections of 750 mg and 1000 mg Testosterone Undecanoate in Hypogonadal Men
NCT00962637PHASE3COMPLETEDStudy to Evaluate the Safety and Efficacy of Androxal™ Treatment in Men With Secondary Hypogonadism
NCT01067365PHASE3COMPLETEDStudy to Evaluate the Safety and Efficacy of Androxal Treatment in Men With Secondary Hypogonadism
NCT01532414PHASE3COMPLETEDPhase III Study to Evaluated Morning Testosterone Normalization in Men With Secondary Hypogonadism
NCT01534208PHASE3COMPLETEDSafety Study of Enclomiphene Citrate in the Treatment of Men With Secondary Hypogonadism
NCT01709331PHASE3COMPLETEDA Study of the Efficacy and Safety of Corifollitropin Alfa (MK-8962) in Combination With Human Chorionic Gonadotropin (hCG) in Adult Men With Hypogonadotropic Hypogonadism (HH) (P07937)