PHC1 polyhomeotic homolog 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PHC1provided by HGNC
Official Full Name: polyhomeotic homolog 1provided by HGNC
Primary source: HGNC:HGNC:3182
See related: Ensembl:ENSG00000111752 MIM:602978; AllianceGenome:HGNC:3182
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: EDR1; HPH1; RAE28; MCPH11
Summary: This gene is a homolog of the Drosophila polyhomeotic gene, which is a member of the Polycomb group of genes. The gene product is a component of a multimeric protein complex that contains EDR2 and the vertebrate Polycomb protein BMH1. The gene product, the EDR2 protein, and the Drosophila polyhomeotic protein share 2 highly conserved domains, named homology domains I and II. These domains are involved in protein-protein interactions and may mediate heterodimerization of the protein encoded by this gene and the EDR2 protein. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 40.0), endometrium (RPKM 27.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.31

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (8913843..8941467)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (8896088..8923703)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (9066439..9094063)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus.
Title: PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus.
These findings reveal several cellular defects in cells carrying the PHC1 mutation and highlight the role of chromatin remodeling in the pathogenesis of PM.
Title: Mutation in PHC1 implicates chromatin remodeling in primary microcephaly pathogenesis.
PcG complex 1, involving Rae28 and Cdt1, supports the activity of hematopoietic stem cells by enhancing cycling capability and hematopoietic activity through direct regulation of Geminin
Title: Polycomb-group complex 1 acts as an E3 ubiquitin ligase for Geminin to sustain hematopoietic stem cell activity.

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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

Associated conditions

Description	Tests
Microcephaly 11, primary, autosomal recessive MedGen: C3809431 OMIM: 615414 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Discovery and refinement of loci associated with lipid levels. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH104 (e-PCR)
- UniSTS:89344

G59818 (e-PCR)
- UniSTS:136967

G27371 (e-PCR)
- UniSTS:48924

G43249 (e-PCR)
- UniSTS:94905

Phc1 (e-PCR), detects polymorphism
- UniSTS:536543

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
involved_in cellular response to retinoic acid	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of PRC1 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of PRC1 complex	IDA Inferred from Direct Assay more info	PubMed
part_of PcG protein complex	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear body	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in sex chromatin	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: polyhomeotic-like protein 1

Names: early development regulator 1 (homolog of polyhomeotic 1); early development regulatory protein 1; polyhomeotic-like 1

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.

Genomic

NG_042273.1 RefSeqGene

Range

4790..31748

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001413738.1 → NP_001400667.1 polyhomeotic-like protein 1 isoform a

Status: REVIEWED

Source sequence(s)

AC006581

UniProtKB/Swiss-Prot

D3DUV4, P78364, Q8WVM3, Q9BU63
NM_001413739.1 → NP_001400668.1 polyhomeotic-like protein 1 isoform b

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413740.1 → NP_001400669.1 polyhomeotic-like protein 1 isoform c

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413741.1 → NP_001400670.1 polyhomeotic-like protein 1 isoform d

Status: REVIEWED

Source sequence(s)

AC006581

Related

ENSP00000399194.2, ENST00000433083.6
NM_001413742.1 → NP_001400671.1 polyhomeotic-like protein 1 isoform e

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413743.1 → NP_001400672.1 polyhomeotic-like protein 1 isoform f

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413744.1 → NP_001400673.1 polyhomeotic-like protein 1 isoform g

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413745.1 → NP_001400674.1 polyhomeotic-like protein 1 isoform h

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413746.1 → NP_001400675.1 polyhomeotic-like protein 1 isoform i

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413747.1 → NP_001400676.1 polyhomeotic-like protein 1 isoform j

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413748.1 → NP_001400677.1 polyhomeotic-like protein 1 isoform k

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413749.1 → NP_001400678.1 polyhomeotic-like protein 1 isoform k

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413750.1 → NP_001400679.1 polyhomeotic-like protein 1 isoform l

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413751.1 → NP_001400680.1 polyhomeotic-like protein 1 isoform m

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413752.1 → NP_001400681.1 polyhomeotic-like protein 1 isoform m

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413753.1 → NP_001400682.1 polyhomeotic-like protein 1 isoform n

Status: REVIEWED

Source sequence(s)

AC006581
NM_001413754.1 → NP_001400683.1 polyhomeotic-like protein 1 isoform o

Status: REVIEWED

Source sequence(s)

AC006581
NM_004426.3 → NP_004417.2 polyhomeotic-like protein 1 isoform a

See identical proteins and their annotated locations for NP_004417.2

Status: REVIEWED

Source sequence(s)

AC006581, BC073964, BM473731, BX640639, CN388283, CN388285, CN388316, U89277

Consensus CDS

CCDS8597.1

UniProtKB/Swiss-Prot

D3DUV4, P78364, Q8WVM3, Q9BU63

UniProtKB/TrEMBL

B2RXH1

Related

ENSP00000437659.1, ENST00000544916.6

Conserved Domains (4) summary

cd09577
Location:935 → 1003

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

smart00454
Location:937 → 1004

SAM; Sterile alpha motif

pfam06467
Location:792 → 827

zf-FCS; MYM-type Zinc finger with FCS sequence motif

pfam16616
Location:828 → 934

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

RNA

NR_182209.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC006581

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

8913843..8941467

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011520603.3 → XP_011518905.1 polyhomeotic-like protein 1 isoform X1

See identical proteins and their annotated locations for XP_011518905.1

UniProtKB/TrEMBL

B2RXH1

Conserved Domains (4) summary

cd09577
Location:952 → 1020

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

smart00454
Location:954 → 1021

SAM; Sterile alpha motif

pfam06467
Location:809 → 844

zf-FCS; MYM-type Zinc finger with FCS sequence motif

pfam16616
Location:845 → 951

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
XM_011520599.3 → XP_011518901.1 polyhomeotic-like protein 1 isoform X2

UniProtKB/TrEMBL

B2RXH1

Conserved Domains (4) summary

cd09577
Location:944 → 1012

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

smart00454
Location:946 → 1013

SAM; Sterile alpha motif

pfam06467
Location:801 → 836

zf-FCS; MYM-type Zinc finger with FCS sequence motif

pfam16616
Location:837 → 943

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
XM_011520600.3 → XP_011518902.1 polyhomeotic-like protein 1 isoform X3

UniProtKB/TrEMBL

B2RXH1

Conserved Domains (4) summary

cd09577
Location:902 → 970

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

smart00454
Location:904 → 971

SAM; Sterile alpha motif

pfam06467
Location:759 → 794

zf-FCS; MYM-type Zinc finger with FCS sequence motif

pfam16616
Location:795 → 901

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
XM_017018957.2 → XP_016874446.1 polyhomeotic-like protein 1 isoform X4

UniProtKB/TrEMBL

B2RXH1
XM_047428475.1 → XP_047284431.1 polyhomeotic-like protein 1 isoform X1
XM_017018955.3 → XP_016874444.1 polyhomeotic-like protein 1 isoform X1

UniProtKB/TrEMBL

B2RXH1

Conserved Domains (4) summary

cd09577
Location:952 → 1020

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

smart00454
Location:954 → 1021

SAM; Sterile alpha motif

pfam06467
Location:809 → 844

zf-FCS; MYM-type Zinc finger with FCS sequence motif

pfam16616
Location:845 → 951

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2