Gene Gene information from NCBI Gene database.
Entrez ID 84295
Gene name PHD finger protein 6
Gene symbol PHF6
Synonyms (NCBI Gene)
BFLSBORJCENP-31
Chromosome X
Chromosome location Xq26.2
Summary This gene is a member of the plant homeodomain (PHD)-like finger (PHF) family. It encodes a protein with two PHD-type zinc finger domains, indicating a potential role in transcriptional regulation, that localizes to the nucleolus. Mutations affecting the
SNPs SNP information provided by dbSNP.
27
SNP ID Visualize variation Clinical significance Consequence
rs104894917 A>G Pathogenic Coding sequence variant, missense variant
rs104894918 A>G Pathogenic Coding sequence variant, missense variant
rs104894919 A>G Pathogenic Coding sequence variant, missense variant
rs112199174 C>T Conflicting-interpretations-of-pathogenicity, benign Coding sequence variant, synonymous variant, genic downstream transcript variant
rs132630297 C>A,T Pathogenic Coding sequence variant, synonymous variant, stop gained, genic downstream transcript variant
miRNA miRNA information provided by mirtarbase database.
471
miRTarBase ID miRNA Experiments Reference
MIRT020833 hsa-miR-155-5p Proteomics 18668040
MIRT022787 hsa-miR-124-3p Proteomics 18668037
MIRT024322 hsa-miR-215-5p Microarray 19074876
MIRT026628 hsa-miR-192-5p Microarray 19074876
MIRT052389 hsa-let-7a-5p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
24
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 24554700
GO:0000775 Component Chromosome, centromeric region IEA
GO:0000776 Component Kinetochore IEA
GO:0001835 Process Blastocyst hatching IEA
GO:0003677 Function DNA binding IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
300414 18145 ENSG00000156531
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q8IWS0
Protein name PHD finger protein 6 (PHD-like zinc finger protein)
Protein function Transcriptional regulator that associates with ribosomal RNA promoters and suppresses ribosomal RNA (rRNA) transcription.
PDB 4NN2 , 4R7A
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF13771 zf-HC5HC2H 42 132 Domain
PF13771 zf-HC5HC2H 239 330 Domain
Tissue specificity TISSUE SPECIFICITY: Ubiquitously expressed. {ECO:0000269|PubMed:12415272}.
Sequence
MSSSVEQKKGPTRQRKCGFCKSNRDKECGQLLISENQKVAAHHKCMLFSSALVSSHSDNE
SLGGFSIEDVQKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYHCALHDKAQIREKPS
QGIYMVYCRKHK
KTAHNSEADLEESFNEHELEPSSPKSKKKSRKGRPRKTNFKGLSEDTR
STSSHGTDEMESSSYRDRSPHRSSPSDTRPKCGFCHVGEEENEARGKLHIFNAKKAAAHY
KCMLFSSGTVQLTTTSRAEFGDFDIKTVLQEIKRGKRMKCTLCSQPGATIGCEIKACVKT
YHYHCGVQDKAKYIENMSRGIYKLYCKNHS
GNDERDEEDEERESKSRGKVEIDQQQLTQQ
QLNGN
Sequence length 365
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG 
  ATP-dependent chromatin remodeling  
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
21
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Borjeson-Forssman-Lehmann syndrome Pathogenic; Likely pathogenic rs770811341, rs2124252847, rs587777489, rs2520644434, rs864309532, rs2520543281, rs1114167289, rs2520470317, rs2077467203, rs132630297, rs132630298, rs104894917, rs132630299, rs104894918, rs132630300
View all (16 more)
RCV001775393
RCV001782610
RCV000128447
RCV002291089
RCV000202613
View all (26 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hereditary spastic paraplegia 4 Pathogenic rs132630300 RCV002286694
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hirsutism Pathogenic rs758791658 RCV001261281
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability Pathogenic; Likely pathogenic rs132630297, rs2077504269, rs758791658 RCV005251034
RCV001257662
RCV001261281
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
CONGENITAL FUSION OF RIBS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CONGENITAL HYPOPLASIA OF PENIS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CONGESTIVE HEART FAILURE Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
DEVELOPMENTAL DISABILITIES Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
2-3 toe syndactyly Syndactyly Of The Toes CLINVAR_DG
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia BEFREE 21736506
★☆☆☆☆
Found in Text Mining only
Acute myeloid leukemia, minimal differentiation Myeloid Leukemia BEFREE 31000771
★☆☆☆☆
Found in Text Mining only
Acute Undifferentiated Leukemia Leukemia BEFREE 21736506
★☆☆☆☆
Found in Text Mining only
Adult Acute Myeloblastic Leukemia Myeloblastic Leukemia BEFREE 21030981
★☆☆☆☆
Found in Text Mining only
Alzheimer Disease Alzheimer disease Pubtator 34209408, 34375027, 34838590 Associate
★☆☆☆☆
Found in Text Mining only
Amyloidosis Amyloidosis BEFREE 31282646
★☆☆☆☆
Found in Text Mining only
Astigmatism Astigmatism Pubtator 36999477 Associate
★☆☆☆☆
Found in Text Mining only
Ataxia Telangiectasia Ataxia telangiectasia Pubtator 27602765 Associate
★☆☆☆☆
Found in Text Mining only
Atrial Septal Defects Atrial Septal Defect CLINVAR_DG
★☆☆☆☆
Found in Text Mining only