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PHTF2

gene
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Also known as DKFZp434D166

Summary

PHTF2 (putative homeodomain transcription factor 2, HGNC:13411) is a protein-coding gene on chromosome 7q11.23-q21.11, encoding Protein PHTF2 (Q8N3S3).

Located in endoplasmic reticulum.

Source: NCBI Gene 57157 — RefSeq curated summary.

At a glance

  • GWAS associations: 25
  • Clinical variants (ClinVar): 124 total
  • MANE Select transcript: NM_001395272

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13411
Approved symbolPHTF2
Nameputative homeodomain transcription factor 2
Location7q11.23-q21.11
Locus typegene with protein product
StatusApproved
AliasesDKFZp434D166
Ensembl geneENSG00000006576
Ensembl biotypeprotein_coding
OMIM616785
Entrez57157

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 22 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000248550, ENST00000275575, ENST00000307305, ENST00000415251, ENST00000416283, ENST00000422959, ENST00000424760, ENST00000450574, ENST00000454592, ENST00000468351, ENST00000470215, ENST00000479515, ENST00000888882, ENST00000888883, ENST00000888884, ENST00000888885, ENST00000888886, ENST00000888887, ENST00000888888, ENST00000888889, ENST00000937835, ENST00000968114, ENST00000968115, ENST00000968116, ENST00000968117, ENST00000968118

RefSeq mRNA: 17 — MANE Select: NM_001395272 NM_001127357, NM_001127358, NM_001127359, NM_001127360, NM_001366081, NM_001366082, NM_001366083, NM_001366084, NM_001366085, NM_001366086, NM_001366087, NM_001366088, NM_001366089, NM_001395270, NM_001395271, NM_001395272, NM_020432

CCDS: CCDS47621, CCDS47622, CCDS47623, CCDS47624, CCDS94132, CCDS94133, CCDS94134

Canonical transcript exons

ENST00000422959 — 19 exons

ExonStartEnd
ENSE000006981337790071177900780
ENSE000006982257793771077937838
ENSE000008770197790176277901920
ENSE000008770267794052877940659
ENSE000009188607789360877893664
ENSE000011272847794003077940302
ENSE000015326817784022177840300
ENSE000018166757779877377798971
ENSE000019365257795485877957225
ENSE000024856827789398277893993
ENSE000035427457795376977953894
ENSE000035436787792262377922778
ENSE000035625347790879377908958
ENSE000035708857795161777951712
ENSE000035865687794967877949833
ENSE000035909037792027977920465
ENSE000036104287792910977929327
ENSE000036424227794270077942786
ENSE000036902417791024577910409

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 99.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.2534 / max 227.7866, expressed in 1802 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
7922310.24391746
792228.29031627
792240.8101506
792260.3725188
792250.2963121
792270.240335

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tibiaUBERON:000097999.13gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451198.88gold quality
biceps brachiiUBERON:000150798.77gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450298.46gold quality
triceps brachiiUBERON:000150997.82gold quality
gluteal muscleUBERON:000200097.79gold quality
diaphragmUBERON:000110397.77gold quality
amniotic fluidUBERON:000017397.45gold quality
skeletal muscle tissueUBERON:000113497.41gold quality
vastus lateralisUBERON:000137997.34gold quality
deltoidUBERON:000147696.96gold quality
quadriceps femorisUBERON:000137796.86gold quality
muscle organUBERON:000163095.36gold quality
skeletal muscle organUBERON:001489295.36gold quality
tendon of biceps brachiiUBERON:000818895.26gold quality
tibialis anteriorUBERON:000138595.23gold quality
body of tongueUBERON:001187695.16gold quality
cartilage tissueUBERON:000241895.14gold quality
muscle tissueUBERON:000238594.86gold quality
parietal pleuraUBERON:000240094.64gold quality
muscle of legUBERON:000138394.62gold quality
gastrocnemiusUBERON:000138894.52gold quality
hindlimb stylopod muscleUBERON:000425294.41gold quality
visceral pleuraUBERON:000240194.35gold quality
pleuraUBERON:000097794.18gold quality
germinal epithelium of ovaryUBERON:000130493.44gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099193.22gold quality
tongueUBERON:000172392.92gold quality
secondary oocyteCL:000065592.86gold quality
endothelial cellCL:000011592.75silver quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-CURD-89yes664.39
E-GEOD-83139yes8.44
E-ANND-3yes5.66

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

202 targeting PHTF2, 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-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-340-5P100.0072.504437
HSA-MIR-4262100.0073.263931
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3163100.0077.238605
HSA-MIR-4692100.0067.322066
HSA-MIR-5692A100.0074.406850
HSA-MIR-656-3P100.0072.152788
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-190A-3P100.0080.355520
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-453499.9966.581907
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-451499.9967.101870
HSA-MIR-428299.9975.366408
HSA-MIR-548AW99.9972.573559
HSA-MIR-186-5P99.9970.833707
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriophtf2ENSDARG00000102123
mus_musculusPhtf2ENSMUSG00000039987
rattus_norvegicusPhtf2ENSRNOG00000013517
drosophila_melanogasterphtfFBGN0028579

Paralogs (1): PHTF1 (ENSG00000116793)

Protein

Protein identifiers

Protein PHTF2 — Q8N3S3 (reviewed: Q8N3S3)

All UniProt accessions (1): Q8N3S3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (7)

UniProt IDNamesCanonical?
Q8N3S3-11yes
Q8N3S3-22
Q8N3S3-33
Q8N3S3-44
Q8N3S3-55
Q8N3S3-66
Q8N3S3-77

RefSeq proteins (17): NP_001120829, NP_001120830, NP_001120831, NP_001120832, NP_001353010, NP_001353011, NP_001353012, NP_001353013, NP_001353014, NP_001353015, NP_001353016, NP_001353017, NP_001353018, NP_001382199, NP_001382200, NP_001382201, NP_065165 (=MANE)

Domains & families (InterPro)

IDNameType
IPR021980PHTF1/2_NDomain
IPR039775PHTF1/2Family

Pfam: PF12129

UniProt features (31 total): transmembrane region 7, compositionally biased region 7, splice variant 7, glycosylation site 3, sequence conflict 3, region of interest 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N3S3-F160.230.07

Functional residue map

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

Glycosylation sites (3): 329, 697, 756

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 374 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, TGCACTT_MIR519C_MIR519B_MIR519A, AAGCCAT_MIR135A_MIR135B, TACAATC_MIR508, BILD_E2F3_ONCOGENIC_SIGNATURE, FOXJ2_01, ATTACAT_MIR3803P, HFH4_01, GENTILE_UV_HIGH_DOSE_DN, HFH3_01, TCCAGAT_MIR5165P, FREAC4_01, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, FISCHER_DREAM_TARGETS

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

1378 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PHTF2POLR3DP05423443
PHTF2TMEM60Q9H2L4433
PHTF2FUNDC2Q9BWH2411
PHTF2SHPRHQ149N8406
PHTF2OTOP1Q7RTM1395
PHTF2CLMPQ9H6B4394
PHTF2ARID3BQ8IVW6385
PHTF2ZFYVE26Q68DK2384
PHTF2YOD1Q5VVQ6361
PHTF2ZNF41P51814360
PHTF2ZNF846Q147U1358
PHTF2LRRIQ4A6NIV6355
PHTF2AIRIMQ9NX04348
PHTF2CFAP95Q5VTT2348
PHTF2SLC35D4Q24JQ0347

IntAct

17 interactions, top by confidence:

ABTypeScore
CSNK2BNMT2psi-mi:“MI:0914”(association)0.660
GPR156PLD2psi-mi:“MI:0914”(association)0.640
B3GAT3GOLIM4psi-mi:“MI:0914”(association)0.640
LYPD3SCAMP1psi-mi:“MI:0914”(association)0.640
PHTF2DHRS2psi-mi:“MI:0915”(physical association)0.400
TTYH1TMEM223psi-mi:“MI:0914”(association)0.350
LYPD3TNPO2psi-mi:“MI:0914”(association)0.350
PHTF2STXBP1psi-mi:“MI:0914”(association)0.350
PHTF2OSBPL3psi-mi:“MI:0914”(association)0.350
CXCR4ESYT2psi-mi:“MI:0914”(association)0.350
FBXW11HNRNPDLpsi-mi:“MI:0914”(association)0.350
PACC1IPO5psi-mi:“MI:0914”(association)0.350
SSMEM1psi-mi:“MI:0914”(association)0.350
SLC27A6NBASpsi-mi:“MI:0914”(association)0.350
PHTF2uxuApsi-mi:“MI:0915”(physical association)0.000
PHTF2psi-mi:“MI:0915”(physical association)0.000

BioGRID (21): PHTF2 (Affinity Capture-MS), PHTF2 (Affinity Capture-MS), PHTF2 (Affinity Capture-MS), PHTF2 (Affinity Capture-RNA), PHTF2 (Affinity Capture-RNA), PHTF2 (Proximity Label-MS), OSBPL6 (Affinity Capture-MS), PHTF2 (Affinity Capture-MS), STXBP2 (Affinity Capture-MS), STXBP1 (Affinity Capture-MS), OSBPL3 (Affinity Capture-MS), VAPA (Affinity Capture-MS), PHTF1 (Affinity Capture-MS), PHTF2 (Affinity Capture-MS), PHTF2 (Affinity Capture-MS)

ESM2 similar proteins: A0JPH4, A3KFU9, A6H7H1, A7UA95, B9U3F2, D3ZWZ9, D4A6L0, E1BBQ2, F1M8G0, O15040, O54828, O75129, O88974, P49805, P97260, Q00M95, Q12770, Q13370, Q14432, Q15047, Q3B7M3, Q3B7T1, Q4ZIN3, Q5MNU5, Q5R9R1, Q5T848, Q5VW38, Q5ZKN3, Q61409, Q62865, Q63085, Q6A0A9, Q6F6B3, Q6GQV7, Q6L8S8, Q6P6V6, Q6PJF5, Q80WQ6, Q80Z10, Q86XL3

Diamond homologs: F1M8G0, Q08DA4, Q5ZKN3, Q8CB19, Q8N3S3, Q9QZ09, Q9UMS5, Q9V9A8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance85
Likely benign5
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3221 predictions. Top by Δscore:

VariantEffectΔscore
7:77840216:CACAG:Cacceptor_loss1.0000
7:77840217:A:AGacceptor_gain1.0000
7:77840218:C:Gacceptor_gain1.0000
7:77840218:CAGC:Cacceptor_loss1.0000
7:77840219:A:AGacceptor_gain1.0000
7:77840220:G:GGacceptor_gain1.0000
7:77840220:GCC:Gacceptor_gain1.0000
7:77840220:GCCT:Gacceptor_gain1.0000
7:77840220:GCCTA:Gacceptor_gain1.0000
7:77840297:GAAG:Gdonor_gain1.0000
7:77840298:AAGG:Adonor_loss1.0000
7:77840300:GGTA:Gdonor_loss1.0000
7:77840301:G:GGdonor_gain1.0000
7:77840301:GTA:Gdonor_loss1.0000
7:77840302:T:Gdonor_loss1.0000
7:77893602:TCATA:Tacceptor_loss1.0000
7:77893605:T:Gacceptor_gain1.0000
7:77893605:TAG:Tacceptor_loss1.0000
7:77893606:A:AGacceptor_gain1.0000
7:77893606:AGAT:Aacceptor_loss1.0000
7:77893606:AGATT:Aacceptor_gain1.0000
7:77893607:G:GGacceptor_gain1.0000
7:77893607:GA:Gacceptor_gain1.0000
7:77893607:GATT:Gacceptor_gain1.0000
7:77893607:GATTG:Gacceptor_gain1.0000
7:77893661:CAAGG:Cdonor_loss1.0000
7:77893663:AG:Adonor_gain1.0000
7:77893663:AGGTA:Adonor_loss1.0000
7:77893664:GG:Gdonor_gain1.0000
7:77893664:GGTAA:Gdonor_loss1.0000

AlphaMissense

4909 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:77893632:T:AW58R1.000
7:77893632:T:CW58R1.000
7:77893634:G:CW58C1.000
7:77893634:G:TW58C1.000
7:77900772:T:CL93P1.000
7:77901770:T:CF99L1.000
7:77901772:T:AF99L1.000
7:77901772:T:GF99L1.000
7:77901818:G:AG115R1.000
7:77901818:G:CG115R1.000
7:77901819:G:AG115E1.000
7:77908885:G:AG180R1.000
7:77908885:G:CG180R1.000
7:77937762:C:AA464D1.000
7:77937770:T:AW467R1.000
7:77937770:T:CW467R1.000
7:77937771:G:CW467S1.000
7:77937772:G:CW467C1.000
7:77937772:G:TW467C1.000
7:77937828:T:AI486K1.000
7:77937828:T:GI486R1.000
7:77940549:T:CF588L1.000
7:77940551:T:AF588L1.000
7:77940551:T:GF588L1.000
7:77940564:T:CS593P1.000
7:77940571:G:TR595M1.000
7:77940572:G:CR595S1.000
7:77940572:G:TR595S1.000
7:77940576:G:CA597P1.000
7:77940577:C:AA597D1.000

dbSNP variants (sampled 300 via entrez): RS1000012720 (7:77876570 A>G), RS1000043950 (7:77916977 A>G), RS1000067081 (7:77843467 T>C), RS1000071578 (7:77867060 A>G), RS1000078084 (7:77888974 G>A,C), RS1000089989 (7:77836365 G>A), RS1000098284 (7:77948525 A>G), RS1000112619 (7:77878444 TGTAGGAGCAACTGGGGA>T,TGTAGGAGCAACTGGGGAGTAGGAGCAACTGGGGA), RS1000134253 (7:77862766 A>G), RS1000159390 (7:77886212 C>T), RS1000176592 (7:77837030 A>G), RS1000203735 (7:77930371 G>T), RS1000223176 (7:77812840 T>C), RS1000270443 (7:77863086 A>C,G), RS1000279691 (7:77834161 A>G)

Disease associations

OMIM: gene MIM:616785 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

25 associations (top):

StudyTraitp-value
GCST000649_15Chronic kidney disease2.000000e-09
GCST001713_10Dental caries2.000000e-06
GCST001762_549Obesity-related traits6.000000e-06
GCST003542_193Night sleep phenotypes8.000000e-06
GCST003790_25Glomerular filtration rate2.000000e-08
GCST005982_3Calcium levels4.000000e-08
GCST006624_55Systolic blood pressure7.000000e-13
GCST007267_43Systolic blood pressure4.000000e-15
GCST007269_271Pulse pressure2.000000e-11
GCST007876_54Estimated glomerular filtration rate1.000000e-15
GCST008059_126Estimated glomerular filtration rate5.000000e-36
GCST008747_103Estimated glomerular filtration rate1.000000e-23
GCST009391_1129Metabolite levels8.000000e-06
GCST009391_1723Metabolite levels9.000000e-06
GCST90020024_104A body shape index2.000000e-11
GCST90020024_105A body shape index3.000000e-11
GCST90020025_1121Waist-to-hip ratio adjusted for BMI5.000000e-15
GCST90020025_1123Waist-to-hip ratio adjusted for BMI1.000000e-15
GCST90020025_351Waist-to-hip ratio adjusted for BMI2.000000e-09
GCST90020025_356Waist-to-hip ratio adjusted for BMI4.000000e-09
GCST90020027_1403Waist-hip index4.000000e-15
GCST90020027_1405Waist-hip index8.000000e-16
GCST90020027_1408Waist-hip index4.000000e-09
GCST90020027_1410Waist-hip index1.000000e-09
GCST90020029_878Waist circumference adjusted for body mass index1.000000e-08

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0003939energy intake
EFO:0004838calcium measurement
EFO:0006335systolic blood pressure
EFO:0005763pulse pressure measurement
EFO:0010456allantoin measurement
EFO:0010341cholesteryl ester 16:0 measurement
EFO:0007789BMI-adjusted waist circumference
EFO:0007788BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression7
bisphenol Aaffects cotreatment, decreases methylation, increases expression2
entinostatdecreases expression, affects cotreatment2
Resveratrolaffects cotreatment, increases expression2
Benzo(a)pyreneincreases methylation, increases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Testosteroneaffects cotreatment, decreases expression2
Aflatoxin B1decreases methylation, increases methylation2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
dicrotophosdecreases expression1
geldanamycinincreases expression1
methylmercuric chloridedecreases expression, increases expression1
triphenyl phosphateaffects expression1
trichostatin Adecreases expression1
arseniteaffects binding, decreases reaction1
mono-(2-ethylhexyl)phthalatedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
cobaltous chloridedecreases expression1
pentanaldecreases expression1
avobenzoneincreases expression1
CGP 52608affects binding, increases reaction1
monomethylarsonous acidincreases expression1
motexafin gadoliniumaffects reaction, increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
ICG 001decreases expression1
Grape Seed Proanthocyanidinsdecreases expression, affects cotreatment1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangdecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): chronic kidney disease, dental caries

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
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BioBTree
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Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot