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PHTF1 putative homeodomain transcription factor 1 [ Homo sapiens (human) ]

Gene ID: 10745, updated on 10-Oct-2023

Summary

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Official Symbol
PHTF1provided by HGNC
Official Full Name
putative homeodomain transcription factor 1provided by HGNC
Primary source
HGNC:HGNC:8939
See related
Ensembl:ENSG00000116793 MIM:604950; AllianceGenome:HGNC:8939
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PHTF
Summary
Predicted to be located in cis-Golgi network and endoplasmic reticulum membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 15.3), gall bladder (RPKM 3.5) and 22 other tissues See more
Orthologs
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Genomic context

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See PHTF1 in Genome Data Viewer
Location:
1p13.2
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (113696831..113759888, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (113708467..113771550, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (114239453..114302510, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene membrane associated guanylate kinase, WW and PDZ domain containing 3 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene Neighboring gene Sharpr-MPRA regulatory region 10793 Neighboring gene MT-ND5 pseudogene 20 Neighboring gene NANOG hESC enhancer GRCh37_chr1:114181286-114181787 Neighboring gene Sharpr-MPRA regulatory region 12988 Neighboring gene NANOG hESC enhancer GRCh37_chr1:114223507-114224045 Neighboring gene ribosomal protein S2 pseudogene 14 Neighboring gene Sharpr-MPRA regulatory region 5734 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:114295082-114295283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114299147-114299702 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1215 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:114301981-114302560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1216 Neighboring gene Sharpr-MPRA regulatory region 4295 Neighboring gene round spermatid basic protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:114353909-114354438 Neighboring gene NANOG-H3K27ac hESC enhancers GRCh37_chr1:114354439-114354968 and GRCh37_chr1:114354969-114355498 Neighboring gene AP4B1 antisense RNA 1 Neighboring gene protein tyrosine phosphatase non-receptor type 22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1538

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Life after log. Siegele DA, et al. J Bacteriol, 1992 Jan. PMID 1729229, Free PMC Article
  2. PHTF, a novel atypical homeobox gene on chromosome 1p13, is evolutionarily conserved. Raich N, et al. Genomics, 1999 Jul 1. PMID 10395808
  3. PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes. Smyth DJ, et al. Diabetes, 2008 Jun. PMID 18305142
  4. Allelic variants in the PHTF1-PTPN22, C12orf30 and CD226 regions as candidate susceptibility factors for the type 1 diabetes in the Estonian population. Douroudis K, et al. BMC Med Genet, 2010 Jan 20. PMID 20089178, Free PMC Article
  5. Molecular characterization of a novel gene family (PHTF) conserved from Drosophila to mammals. Manuel A, et al. Genomics, 2000 Mar 1. PMID 10729229

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  2. Results supports the rs6679677 (PHTF1-PTPN22) SNP as a susceptibility factor for type 1 diabetes.
    Title: Allelic variants in the PHTF1-PTPN22, C12orf30 and CD226 regions as candidate susceptibility factors for the type 1 diabetes in the Estonian population.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Common variants at CD40 and other loci confer risk of rheumatoid arthritis.
EBI GWAS Catalog
Genetic variants associated with disordered eating.
EBI GWAS Catalog
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci.
EBI GWAS Catalog
Novel associations for hypothyroidism include known autoimmune risk loci.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog
Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in cis-Golgi network membrane IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protein PHTF1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001323041.2 → NP_001309970.1  protein PHTF1 isoform a

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321
    Consensus CDS
    CCDS861.1
    UniProtKB/Swiss-Prot
    Q5VWP7, Q5VWP8, Q9BUP2, Q9H1X8, Q9UMS5
    UniProtKB/TrEMBL
    Q5TCQ5
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 149
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  2. NM_001323042.2 → NP_001309971.1  protein PHTF1 isoform a

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321
    Consensus CDS
    CCDS861.1
    UniProtKB/Swiss-Prot
    Q5VWP7, Q5VWP8, Q9BUP2, Q9H1X8, Q9UMS5
    UniProtKB/TrEMBL
    Q5TCQ5
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 149
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  3. NM_001323043.2 → NP_001309972.1  protein PHTF1 isoform a

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321
    Consensus CDS
    CCDS861.1
    UniProtKB/Swiss-Prot
    Q5VWP7, Q5VWP8, Q9BUP2, Q9H1X8, Q9UMS5
    UniProtKB/TrEMBL
    Q5TCQ5
    Related
    ENSP00000358617.1, ENST00000369604.6
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 149
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  4. NM_001323044.2 → NP_001309973.1  protein PHTF1 isoform b

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321
    UniProtKB/TrEMBL
    Q5TCQ5
    Conserved Domains (1) summary
    pfam12129
    Location:1 → 107
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  5. NM_001323045.2 → NP_001309974.1  protein PHTF1 isoform b

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321
    UniProtKB/TrEMBL
    Q5TCQ5
    Conserved Domains (1) summary
    pfam12129
    Location:1 → 107
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  6. NM_001323046.2 → NP_001309975.1  protein PHTF1 isoform c

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321

  7. NM_001323047.2 → NP_001309976.1  protein PHTF1 isoform d

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321
    Consensus CDS
    CCDS81359.1
    UniProtKB/TrEMBL
    Q5TCQ5
    Related
    ENSP00000350428.2, ENST00000357783.6
    Conserved Domains (1) summary
    pfam12129
    Location:6 → 149
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  8. NM_001323048.2 → NP_001309977.1  protein PHTF1 isoform d

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321
    Consensus CDS
    CCDS81359.1
    UniProtKB/TrEMBL
    Q5TCQ5
    Conserved Domains (1) summary
    pfam12129
    Location:6 → 149
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  9. NM_001323049.2 → NP_001309978.1  protein PHTF1 isoform d

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321
    Consensus CDS
    CCDS81359.1
    UniProtKB/TrEMBL
    Q5TCQ5
    Conserved Domains (1) summary
    pfam12129
    Location:6 → 149
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  10. NM_001323050.2 → NP_001309979.1  protein PHTF1 isoform e

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321

  11. NM_001323051.2 → NP_001309980.1  protein PHTF1 isoform f

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321

  12. NM_001323052.2 → NP_001309981.1  protein PHTF1 isoform g

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 149
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  13. NM_001323053.2 → NP_001309982.1  protein PHTF1 isoform g

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 149
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  14. NM_006608.3 → NP_006599.2  protein PHTF1 isoform a

    See identical proteins and their annotated locations for NP_006599.2

    Status: VALIDATED

    Source sequence(s)
    AJ011863, AK126773, AL133517, AL365321, BC002447, CX763183, DA728266, DB457884
    Consensus CDS
    CCDS861.1
    UniProtKB/Swiss-Prot
    Q5VWP7, Q5VWP8, Q9BUP2, Q9H1X8, Q9UMS5
    UniProtKB/TrEMBL
    Q5TCQ5
    Related
    ENSP00000377025.2, ENST00000393357.6
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 149
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

RNA

  1. NR_136564.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321

  2. NR_136565.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321

  3. NR_136566.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321

  4. NR_136567.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321

  5. NR_136568.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL133517, AL365321

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    113696831..113759888 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    113708467..113771550 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UMS5.2 GenPept UniProtKB/Swiss-Prot:Q9UMS5

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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