Q8IWS0 (PHF6_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
PHD finger protein 6

Alternative name(s):
PHD-like zinc finger protein

Gene names

Name:	PHF6
Synonyms:	KIAA1823

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	365 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	May play a role in transcriptional regulation.
Subcellular location	Nucleus. Nucleus › nucleolus. Note: Nuclear, it particularly localizes to the nucleolus. Ref.1
Tissue specificity	Ubiquitously expressed. Ref.1
Involvement in disease	Boerjeson-Forssman-Lehmann syndrome (BFLS) [MIM:301900]: A X-linked recessive disorder characterized by moderate to severe mental retardation, epilepsy, hypogonadism, hypometabolism, obesity with marked gynecomastia, swelling of subcutaneous tissue of the face, narrow palpebral fissure and large but not deformed ears. Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.1
Sequence similarities	Contains 2 PHD-type zinc fingers.
Sequence caution	The sequence BAB47452.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Disease	Disease mutation Epilepsy Mental retardation
Domain	Repeat Zinc-finger
Ligand	Metal-binding Zinc
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleolus Inferred from direct assay. Source: HPA
Molecular_function	zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q8IWS0-1)

Also known as: PHF6a; PHF6b;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q8IWS0-2)

The sequence of this isoform differs from the canonical sequence as follows:
     140-140: A → AA
     279-311: KCTLCSQPGATIGCEIKACVKTYHYHCGVQDKA → VCSFYICYATLHLICCFKFRVHPKFIQSSENLK
     312-365: Missing.

Note: No experimental confirmation available. Contains a phosphoserine at position 146.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 365	365	PHD finger protein 6		PRO_0000059293
Regions
	Zinc finger	79 – 131	53	PHD-type 1; degenerate
	Zinc finger	277 – 329	53	PHD-type 2; degenerate
	Motif	13 – 16	4	Nuclear localization signal Potential
	Motif	129 – 133	5	Nuclear localization signal Potential
	Motif	157 – 169	13	Nucleolar localization signal Potential
Amino acid modifications
	Modified residue	138	1	Phosphoserine Ref.9 Ref.10
	Modified residue	145	1	Phosphoserine Ref.9 Ref.11
	Modified residue	155	1	Phosphoserine Ref.13
	Modified residue	199	1	Phosphoserine Ref.13
	Modified residue	358	1	Phosphothreonine Ref.7
Natural variations
	Alternative sequence	140	1	A → AA in isoform 2.		VSP_009372
	Alternative sequence	279 – 311	33	KCTLC…VQDKA → VCSFYICYATLHLICCFKFR VHPKFIQSSENLK in isoform 2.		VSP_009373
	Alternative sequence	312 – 365	54	Missing in isoform 2.		VSP_009374
	Natural variant	45	1	C → Y in BFLS. Ref.1 Corresponds to variant rs28935179 [ dbSNP | Ensembl ].		VAR_017633
	Natural variant	99	1	C → F in BFLS. Ref.1		VAR_017634
	Natural variant	229	1	H → R in BFLS. Ref.1		VAR_017635
	Natural variant	234	1	K → E in BFLS. Ref.1		VAR_017636
	Natural variant	257	1	R → G in BFLS. Ref.1		VAR_017637
Experimental info
	Sequence conflict	126	1	V → A in AAH05994. Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (PHF6a) (PHF6b) [UniParc]. Last modified March 1, 2003. Version 1. Checksum: E8E587909EF9701D	FASTA	365	41,290
	10 20 30 40 50 60 MSSSVEQKKG PTRQRKCGFC KSNRDKECGQ LLISENQKVA AHHKCMLFSS ALVSSHSDNE 70 80 90 100 110 120 SLGGFSIEDV QKEIKRGTKL MCSLCHCPGA TIGCDVKTCH RTYHYHCALH DKAQIREKPS 130 140 150 160 170 180 QGIYMVYCRK HKKTAHNSEA DLEESFNEHE LEPSSPKSKK KSRKGRPRKT NFKGLSEDTR 190 200 210 220 230 240 STSSHGTDEM ESSSYRDRSP HRSSPSDTRP KCGFCHVGEE ENEARGKLHI FNAKKAAAHY 250 260 270 280 290 300 KCMLFSSGTV QLTTTSRAEF GDFDIKTVLQ EIKRGKRMKC TLCSQPGATI GCEIKACVKT 310 320 330 340 350 360 YHYHCGVQDK AKYIENMSRG IYKLYCKNHS GNDERDEEDE ERESKSRGKV EIDQQQLTQQ QLNGN
	Isoform 2 [UniParc]. Checksum: 107F45F45063D7A0	FASTA	312	35,329
	10 20 30 40 50 60 MSSSVEQKKG PTRQRKCGFC KSNRDKECGQ LLISENQKVA AHHKCMLFSS ALVSSHSDNE 70 80 90 100 110 120 SLGGFSIEDV QKEIKRGTKL MCSLCHCPGA TIGCDVKTCH RTYHYHCALH DKAQIREKPS 130 140 150 160 170 180 QGIYMVYCRK HKKTAHNSEA ADLEESFNEH ELEPSSPKSK KKSRKGRPRK TNFKGLSEDT 190 200 210 220 230 240 RSTSSHGTDE MESSSYRDRS PHRSSPSDTR PKCGFCHVGE EENEARGKLH IFNAKKAAAH 250 260 270 280 290 300 YKCMLFSSGT VQLTTTSRAE FGDFDIKTVL QEIKRGKRMV CSFYICYATL HLICCFKFRV 310 HPKFIQSSEN LK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Mutations in PHF6 are associated with Boerjeson-Forssman-Lehmann syndrome." Lower K.M., Turner G., Kerr B.A., Mathews K.D., Shaw M.A., Gedeon A.K., Schelley S., Hoyme H.E., White S.M., Delatycki M.B., Lampe A.K., Clayton-Smith J., Stewart H., van Ravenswaay C.M.A., de Vries B.B.A., Cox B., Grompe M., Ross S. , Thomas P., Mulley J.C., Gecz J. Nat. Genet. 32:661-665(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, SUBCELLULAR LOCATION, ALTERNATIVE SPLICING, VARIANTS BFLS TYR-45; PHE-99; ARG-229; GLU-234 AND GLY-257.
[2]	"Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro." Nagase T., Nakayama M., Nakajima D., Kikuno R., Ohara O. DNA Res. 8:85-95(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Brain.
[3]	"The DNA sequence of the human X chromosome." Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C. , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R. Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Tissue: Bone marrow.
[6]	"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma.
[7]	"ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage." Matsuoka S., Ballif B.A., Smogorzewska A., McDonald E.R. III, Hurov K.E., Luo J., Bakalarski C.E., Zhao Z., Solimini N., Lerenthal Y., Shiloh Y., Gygi S.P., Elledge S.J. Science 316:1160-1166(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-358, MASS SPECTROMETRY. Tissue: Embryonic kidney.
[8]	"Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle." Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M. Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma.
[9]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-138 AND SER-145, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-146 (ISOFORM 2), MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[10]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-138, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[11]	"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M. Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-145, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[12]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]	"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation." Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B. Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-155 AND SER-199, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Web resources

GeneReviews

Cross-references

Sequence databases
EMBL GenBank DDBJ	AY157622 mRNA. Translation: AAO13214.1. AB058726 mRNA. Translation: BAB47452.1. Different initiation. AL591668, AC004383 Genomic DNA. Translation: CAI41600.1. AL591668 Genomic DNA. Translation: CAI41601.1. CH471107 Genomic DNA. Translation: EAX11762.1. CH471107 Genomic DNA. Translation: EAX11763.1. CH471107 Genomic DNA. Translation: EAX11766.1. BC005994 mRNA. Translation: AAH05994.1.
IPI	IPI00395568. IPI00397700.
RefSeq	NP_001015877.1. NM_001015877.1. NP_115711.2. NM_032335.3. NP_115834.1. NM_032458.2.
UniGene	Hs.356501.
3D structure databases
ProteinModelPortal	Q8IWS0.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q8IWS0. 2 interactions.
STRING	9606.ENSP00000329097.
PTM databases
PhosphoSite	Q8IWS0.
Polymorphism databases
DMDM	42559482.
Proteomic databases
PaxDb	Q8IWS0.
PeptideAtlas	Q8IWS0.
PRIDE	Q8IWS0.
Protocols and materials databases
DNASU	84295.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000332070; ENSP00000329097; ENSG00000156531. ENST00000370800; ENSP00000359836; ENSG00000156531. ENST00000370803; ENSP00000359839; ENSG00000156531.
GeneID	84295.
KEGG	hsa:84295.
UCSC	uc004exh.3. human. uc004exj.3. human.
Organism-specific databases
CTD	84295.
GeneCards	GC0XP133507.
HGNC	HGNC:18145. PHF6.
HPA	HPA001023.
MIM	300414. gene. 301900. phenotype.
neXtProt	NX_Q8IWS0.
Orphanet	127. Borjeson-Forssman-Lehmann syndrome.
PharmGKB	PA33263.
HUGE	Search...
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG282606.
HOGENOM	HOG000026798.
HOVERGEN	HBG049389.
OrthoDB	EOG4K9BCK.
PhylomeDB	Q8IWS0.
Gene expression databases
ArrayExpress	Q8IWS0.
Bgee	Q8IWS0.
CleanEx	HS_PHF6.
Genevestigator	Q8IWS0.
GermOnline	ENSG00000156531. Homo sapiens.
Family and domain databases
InterPro	IPR001965. Znf_PHD. [Graphical view]
SMART	SM00249. PHD. 2 hits. [Graphical view]
PROSITE	PS01359. ZF_PHD_1. False negative. PS50016. ZF_PHD_2. False negative. [Graphical view]
ProtoNet	Search...
Other
ChiTaRS	PHF6. human.
GenomeRNAi	84295.
NextBio	73944.
SOURCE	Search...

Entry information

Entry name

PHF6_HUMAN

Accession

Primary (citable) accession number: Q8IWS0
Secondary accession number(s): D3DTG3 , Q5JRC7, Q5JRC8, Q96JK3, Q9BRU0

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 16, 2004
Last sequence update:	March 1, 2003
Last modified:	May 1, 2013
This is version 98 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.