PHETA2 (PH domain containing endocytic trafficking adaptor 2) - Rat Genome Database

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Gene: PHETA2 (PH domain containing endocytic trafficking adaptor 2) Homo sapiens
Analyze
Symbol: PHETA2
Name: PH domain containing endocytic trafficking adaptor 2
RGD ID: 1604738
HGNC Page HGNC
Description: Enables protein homodimerization activity. Involved in endosome organization; receptor recycling; and retrograde transport, endosome to Golgi. Located in cytoplasmic vesicle and trans-Golgi network; INTERACTS WITH 17beta-estradiol; aristolochic acid; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 27 kDa inositol polyphosphate phosphatase interacting protein B; DKFZp686J07229; FAM109B; family with sequence similarity 109 member B; family with sequence similarity 109, member B; hypothetical protein LOC150368; inositol polyphosphate phosphatase-interacting protein B; IPIP27B; MGC125831; MGC125832; Ses2; sesquipedalian-2
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2242,074,248 - 42,079,438 (+)EnsemblGRCh38hg38GRCh38
GRCh382242,074,244 - 42,079,438 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372242,470,252 - 42,475,442 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362240,800,201 - 40,805,388 (+)NCBINCBI36hg18NCBI36
Celera2226,276,457 - 26,281,644 (+)NCBI
Cytogenetic Map22q13.2NCBI
HuRef2225,436,442 - 25,441,629 (+)NCBIHuRef
CHM1_12242,430,368 - 42,435,561 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

Additional References at PubMed
PMID:10591208   PMID:12477932   PMID:15461802   PMID:15489334   PMID:18029348   PMID:20133602   PMID:21233288   PMID:21873635   PMID:25056061   PMID:26496610   PMID:26673895   PMID:27107012  
PMID:28514442   PMID:31586073   PMID:32152089   PMID:32296183   PMID:32694731  


Genomics

Comparative Map Data
PHETA2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2242,074,248 - 42,079,438 (+)EnsemblGRCh38hg38GRCh38
GRCh382242,074,244 - 42,079,438 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372242,470,252 - 42,475,442 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362240,800,201 - 40,805,388 (+)NCBINCBI36hg18NCBI36
Celera2226,276,457 - 26,281,644 (+)NCBI
Cytogenetic Map22q13.2NCBI
HuRef2225,436,442 - 25,441,629 (+)NCBIHuRef
CHM1_12242,430,368 - 42,435,561 (+)NCBICHM1_1
Pheta2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391582,223,148 - 82,229,911 (+)NCBIGRCm39mm39
GRCm39 Ensembl1582,223,143 - 82,229,944 (+)Ensembl
GRCm381582,338,927 - 82,345,710 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1582,338,942 - 82,345,743 (+)EnsemblGRCm38mm10GRCm38
MGSCv371582,171,609 - 82,176,140 (+)NCBIGRCm37mm9NCBIm37
MGSCv361582,168,971 - 82,173,474 (+)NCBImm8
Celera1584,465,330 - 84,469,878 (+)NCBICelera
Cytogenetic Map15E1NCBI
Pheta2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27113,855,437 - 113,861,910 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7113,857,249 - 113,861,871 (+)Ensembl
Rnor_6.07123,572,153 - 123,578,590 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,573,930 - 123,578,551 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07123,558,649 - 123,563,270 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47120,716,939 - 120,721,560 (+)NCBIRGSC3.4rn4RGSC3.4
Celera7110,172,088 - 110,176,709 (+)NCBICelera
Cytogenetic Map7q34NCBI
Pheta2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541327,475,658 - 27,480,879 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541327,475,658 - 27,480,879 (+)NCBIChiLan1.0ChiLan1.0
PHETA2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12241,046,587 - 41,057,096 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2241,054,956 - 41,055,735 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02222,964,383 - 22,972,840 (+)NCBIMhudiblu_PPA_v0panPan3
PHETA2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11023,297,522 - 23,303,019 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1023,231,610 - 23,236,585 (-)NCBI
ROS_Cfam_1.01024,042,044 - 24,047,024 (-)NCBI
UMICH_Zoey_3.11023,759,653 - 23,764,627 (-)NCBI
UNSW_CanFamBas_1.01024,080,495 - 24,085,467 (-)NCBI
UU_Cfam_GSD_1.01024,254,477 - 24,259,457 (-)NCBI
Pheta2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049456,924,536 - 6,929,812 (-)NCBI
SpeTri2.0NW_00493671850,354 - 55,699 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHETA2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl56,571,556 - 6,576,870 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.156,571,628 - 6,576,993 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.253,979,641 - 3,986,138 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PHETA2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11924,608,631 - 24,616,343 (+)NCBI
ChlSab1.1 Ensembl1924,614,192 - 24,614,971 (+)Ensembl
Vero_WHO_p1.0NW_023666045100,779,163 - 100,786,365 (-)NCBI
Pheta2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247526,665,433 - 6,675,776 (-)NCBI

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1403
Count of miRNA genes:632
Interacting mature miRNAs:709
Transcripts:ENST00000321753, ENST00000419475
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 2216 1403 634 180 379 36 2977 911 779 147 843 1148 150 1077 1817 2
Low 193 1514 1058 414 1372 398 1352 1261 2793 248 585 406 24 1 127 966 2 2
Below cutoff 23 73 28 25 176 26 24 25 157 16 28 50 1 5 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000321753   ⟹   ENSP00000312753
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2242,074,248 - 42,079,438 (+)Ensembl
RefSeq Acc Id: ENST00000419475   ⟹   ENSP00000396170
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2242,074,357 - 42,077,618 (+)Ensembl
RefSeq Acc Id: NM_001002034   ⟹   NP_001002034
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382242,074,248 - 42,079,438 (+)NCBI
GRCh372242,470,255 - 42,475,445 (+)NCBI
Build 362240,800,201 - 40,805,388 (+)NCBI Archive
Celera2226,276,457 - 26,281,644 (+)RGD
HuRef2225,436,442 - 25,441,629 (+)RGD
CHM1_12242,430,368 - 42,435,561 (+)NCBI
Sequence:
RefSeq Acc Id: XM_005261373   ⟹   XP_005261430
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382242,074,244 - 42,079,438 (+)NCBI
GRCh372242,470,255 - 42,475,445 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001002034   ⟸   NM_001002034
- UniProtKB: Q6ICB4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_005261430   ⟸   XM_005261373
- Peptide Label: isoform X1
- UniProtKB: Q6ICB4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000312753   ⟸   ENST00000321753
RefSeq Acc Id: ENSP00000396170   ⟸   ENST00000419475
Protein Domains
PH

Promoters
RGD ID:6799973
Promoter ID:HG_KWN:43045
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3,   Lymphoblastoid
Transcripts:OTTHUMT00000322084,   OTTHUMT00000322085
Position:
Human AssemblyChrPosition (strand)Source
Build 362240,800,171 - 40,800,671 (+)MPROMDB
RGD ID:13604306
Promoter ID:EPDNEW_H28336
Type:initiation region
Name:FAM109B_1
Description:family with sequence similarity 109 member B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382242,074,264 - 42,074,324EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 22q12.3-13.33(chr22:33768441-50739977)x3 copy number gain See cases [RCV000051682] Chr22:33768441..50739977 [GRCh38]
Chr22:34164428..51178405 [GRCh37]
Chr22:32494428..49525271 [NCBI36]
Chr22:22q12.3-13.33
pathogenic
GRCh38/hg38 22q12.3-13.33(chr22:37061769-50738932)x3 copy number gain See cases [RCV000051684] Chr22:37061769..50738932 [GRCh38]
Chr22:37457809..51177360 [GRCh37]
Chr22:35787755..49524226 [NCBI36]
Chr22:22q12.3-13.33
pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916608-50739836)x3 copy number gain See cases [RCV000133646] Chr22:16916608..50739836 [GRCh38]
Chr22:17397498..51178264 [GRCh37]
Chr22:15777498..49525130 [NCBI36]
Chr22:22q11.1-13.33
pathogenic
Single allele deletion Intellectual disability [RCV001293368] Chr22:42356886..43684002 [GRCh37]
Chr22:22q13.2
pathogenic
Single allele deletion Intellectual disability [RCV001293376] Chr22:42333802..51195728 [GRCh37]
Chr22:22q13.2-13.33
pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916743-50739785)x3 copy number gain See cases [RCV000134730] Chr22:16916743..50739785 [GRCh38]
Chr22:17397633..51178213 [GRCh37]
Chr22:15777633..49525079 [NCBI36]
Chr22:22q11.1-13.33
pathogenic
GRCh38/hg38 22q13.1-13.33(chr22:40202014-50735806)x3 copy number gain See cases [RCV000134513] Chr22:40202014..50735806 [GRCh38]
Chr22:40598018..51174234 [GRCh37]
Chr22:38927964..49521100 [NCBI36]
Chr22:22q13.1-13.33
pathogenic
GRCh38/hg38 22q13.2(chr22:41645339-42565798)x1 copy number loss See cases [RCV000136528] Chr22:41645339..42565798 [GRCh38]
Chr22:42041343..42961804 [GRCh37]
Chr22:40371289..41291748 [NCBI36]
Chr22:22q13.2
uncertain significance
GRCh38/hg38 22q13.2-13.33(chr22:41871143-50739836)x1 copy number loss See cases [RCV000136921] Chr22:41871143..50739836 [GRCh38]
Chr22:42267147..51178264 [GRCh37]
Chr22:40597093..49525130 [NCBI36]
Chr22:22q13.2-13.33
pathogenic
GRCh38/hg38 22q13.2(chr22:41277822-42414957)x3 copy number gain See cases [RCV000136785] Chr22:41277822..42414957 [GRCh38]
Chr22:41673826..42810963 [GRCh37]
Chr22:40003772..41140907 [NCBI36]
Chr22:22q13.2
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51237518)x3 copy number gain See cases [RCV000240091] Chr22:16054691..51237518 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q13.2(chr22:42207144-42776457)x1 copy number loss See cases [RCV000240146] Chr22:42207144..42776457 [GRCh37]
Chr22:22q13.2
uncertain significance
GRCh37/hg19 22q12.3-13.33(chr22:35728929-51220961)x3 copy number gain See cases [RCV000240469] Chr22:35728929..51220961 [GRCh37]
Chr22:22q12.3-13.33
pathogenic
GRCh37/hg19 22q13.1-13.33(chr22:40425714-51220961)x3 copy number gain See cases [RCV000240459] Chr22:40425714..51220961 [GRCh37]
Chr22:22q13.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51220902)x3 copy number gain See cases [RCV000446956] Chr22:16054691..51220902 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51237463)x3 copy number gain See cases [RCV000448847] Chr22:16054691..51237463 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q13.2(chr22:42458857-42474106)x3 copy number gain See cases [RCV000448223] Chr22:42458857..42474106 [GRCh37]
Chr22:22q13.2
likely benign
GRCh37/hg19 22q13.2(chr22:41835094-42756616)x3 copy number gain See cases [RCV000511241] Chr22:41835094..42756616 [GRCh37]
Chr22:22q13.2
uncertain significance
GRCh37/hg19 22q13.2-13.33(chr22:42441918-51197838)x1 copy number loss See cases [RCV000510765] Chr22:42441918..51197838 [GRCh37]
Chr22:22q13.2-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16888900-51197838) copy number gain See cases [RCV000510873] Chr22:16888900..51197838 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16888900-51197838)x3 copy number gain See cases [RCV000512333] Chr22:16888900..51197838 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q13.2(chr22:41849322-42756616)x3 copy number gain not provided [RCV000684486] Chr22:41849322..42756616 [GRCh37]
Chr22:22q13.2
likely pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054667-51243435)x3 copy number gain not provided [RCV000741689] Chr22:16054667..51243435 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16114244-51195728)x3 copy number gain not provided [RCV000741691] Chr22:16114244..51195728 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:42151555-51195728)x1 copy number loss not provided [RCV000741989] Chr22:42151555..51195728 [GRCh37]
Chr22:22q13.2-13.33
pathogenic
GRCh37/hg19 22q13.2(chr22:42470317-42535461)x1 copy number loss not provided [RCV000741995] Chr22:42470317..42535461 [GRCh37]
Chr22:22q13.2
benign
GRCh37/hg19 22q11.1-13.33(chr22:16114244-51211392)x3 copy number gain not provided [RCV000741692] Chr22:16114244..51211392 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:42416026-51181759) copy number loss 22q13.3 deletion syndrome [RCV000767745] Chr22:42416026..51181759 [GRCh37]
Chr22:22q13.2-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16888899-51197838)x3 copy number gain not provided [RCV000846344] Chr22:16888899..51197838 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q12.2-13.33(chr22:30654764-51197838)x3 copy number gain not provided [RCV001007181] Chr22:30654764..51197838 [GRCh37]
Chr22:22q12.2-13.33
pathogenic
GRCh37/hg19 22q13.1-13.33(chr22:40502364-51197838)x3 copy number gain not provided [RCV001007502] Chr22:40502364..51197838 [GRCh37]
Chr22:22q13.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16197005-51224252)x3 copy number gain See cases [RCV001263056] Chr22:16197005..51224252 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
Single allele deletion Developmental delay with variable intellectual impairment and behavioral abnormalities [RCV001391668] Chr22:42440000..43780000 [GRCh37]
Chr22:22q13.2
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:27161 AgrOrtholog
COSMIC PHETA2 COSMIC
Ensembl Genes ENSG00000177096 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000312753 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000396170 UniProtKB/TrEMBL
Ensembl Transcript ENST00000321753 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000419475 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000177096 GTEx
HGNC ID HGNC:27161 ENTREZGENE
Human Proteome Map PHETA2 Human Proteome Map
InterPro PH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:150368 UniProtKB/Swiss-Prot
NCBI Gene 150368 ENTREZGENE
OMIM 614240 OMIM
Pfam PF00169 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA143485467 PharmGKB
PROSITE PH_DOMAIN UniProtKB/Swiss-Prot
SMART SM00233 UniProtKB/Swiss-Prot
UniProt B1AHR3_HUMAN UniProtKB/TrEMBL
  Q6ICB4 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q3SXQ3 UniProtKB/Swiss-Prot
  Q8N6L9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-02-27 PHETA2  PH domain containing endocytic trafficking adaptor 2  FAM109B  family with sequence similarity 109 member B  Symbol and/or name change 5135510 APPROVED
2015-11-24 FAM109B  family with sequence similarity 109 member B    family with sequence similarity 109, member B  Symbol and/or name change 5135510 APPROVED