PROM1 prominin 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PROM1provided by HGNC
Official Full Name: prominin 1provided by HGNC
Primary source: HGNC:HGNC:9454
See related: Ensembl:ENSG00000007062 MIM:604365; AllianceGenome:HGNC:9454
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: RP41; AC133; CD133; MCDR2; STGD4; CORD12; PROML1; MSTP061
Summary: This gene encodes a pentaspan transmembrane glycoprotein. The protein localizes to membrane protrusions and is often expressed on adult stem cells, where it is thought to function in maintaining stem cell properties by suppressing differentiation. Mutations in this gene have been shown to result in retinitis pigmentosa and Stargardt disease. Expression of this gene is also associated with several types of cancer. This gene is expressed from at least five alternative promoters that are expressed in a tissue-dependent manner. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
Expression: Broad expression in gall bladder (RPKM 15.7), stomach (RPKM 10.2) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4p15.32

Exon count:: 34

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (15968228..16084023, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (15949919..16107700, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (15969851..16085646, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Deciphering the impact of PROM1 alternative splicing on human photoreceptor development and maturation.
Title: Deciphering the impact of PROM1 alternative splicing on human photoreceptor development and maturation.
Clinical exome analysis and targeted gene repair of the c.1354dupT variant in iPSC lines from patients with PROM1-related retinopathies exhibiting diverse phenotypes.
Title: Clinical exome analysis and targeted gene repair of the c.1354dupT variant in iPSC lines from patients with PROM1-related retinopathies exhibiting diverse phenotypes.
CD133 Stimulates Cell Proliferation via the Upregulation of Amphiregulin in Melanoma.
Title: CD133 Stimulates Cell Proliferation via the Upregulation of Amphiregulin in Melanoma.
Deep phenotyping of PROM1-associated retinal degeneration.
Title: Deep phenotyping of PROM1-associated retinal degeneration.
High CD133 expression in proximal tubular cells in diabetic kidney disease: good or bad?
Title: High CD133 expression in proximal tubular cells in diabetic kidney disease: good or bad?
Emergence of bedaquiline-resistant tuberculosis and of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis strains with rpoB Ile491Phe mutation not detected by Xpert MTB/RIF in Mozambique: a retrospective observational study.
Title: Emergence of bedaquiline-resistant tuberculosis and of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis strains with rpoB Ile491Phe mutation not detected by Xpert MTB/RIF in Mozambique: a retrospective observational study.
CD133, CD47, and PD-L1 Expression in Ovarian High-grade Serous Carcinoma and Its Association with Metastatic Disease: A Cross-sectional Study.
Title: CD133, CD47, and PD-L1 Expression in Ovarian High-grade Serous Carcinoma and Its Association with Metastatic Disease: A Cross-sectional Study.
Impact of heterogeneous nuclear ribonucleoprotein A/B subtype overexpression on the expression of cancer stem cell markers CD133 and CD44 and cellular proliferation capacity.
Title: Impact of heterogeneous nuclear ribonucleoprotein A/B subtype overexpression on the expression of cancer stem cell markers CD133 and CD44 and cellular proliferation capacity.
Functional Roles of CD133: More than Stemness Associated Factor Regulated by the Microenvironment.
Title: Functional Roles of CD133: More than Stemness Associated Factor Regulated by the Microenvironment.
Genetic and clinical characteristics of PROM1-related retinal degeneration in Korean.
Title: Genetic and clinical characteristics of PROM1-related retinal degeneration in Korean.

Submit: New GeneRIF Correction See all GeneRIFs (588)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Cone-rod dystrophy 12 MedGen: C2675210 OMIM: 612657 GeneReviews: Not available	Compare labs
Retinal macular dystrophy type 2 MedGen: C4749334 OMIM: 608051 GeneReviews: Not available	Compare labs
Retinitis pigmentosa 41 MedGen: C2677516 OMIM: 612095 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview	Compare labs
Stargardt disease 4 MedGen: C1863534 OMIM: 603786 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide association study of self-rated health. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic relationships between suicide attempts, suicidal ideation and major psychiatric disorders: a genome-wide association and polygenic scoring study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association studies of pit-and-fissure- and smooth-surface caries in permanent dentition. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS of dental caries patterns in the permanent dentition. 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

RH121881 (e-PCR)
- UniSTS:137735

D4S2397 (e-PCR)
- UniSTS:28186

G33894 (e-PCR)
- UniSTS:17979

SHGC-7038 (e-PCR)
- UniSTS:18497

WI-22012 (e-PCR)
- UniSTS:18249

SHGC4-910 (e-PCR)
- UniSTS:73291

D4S1601 (e-PCR)
- UniSTS:3412

D4S403 (e-PCR), detects polymorphism
- UniSTS:15705

D4S3023 (e-PCR), detects polymorphism
- UniSTS:9328

D4S497 (e-PCR)
- UniSTS:24177

SHGC-141874 (e-PCR)
- UniSTS:171131

D4S3048 (e-PCR)
- UniSTS:34172

D4S1582 (e-PCR), detects polymorphism
- UniSTS:18313

D4S3022 (e-PCR), detects polymorphism
- UniSTS:48272

SHGC-147822 (e-PCR)
- UniSTS:176033

SHGC-149115 (e-PCR)
- UniSTS:176808

D4S391 (e-PCR), detects polymorphism
- UniSTS:24233

G16721 (e-PCR)
- UniSTS:76723

SHGC-24088 (e-PCR)
- UniSTS:31690

G62790 (e-PCR)
- UniSTS:139767

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actinin binding	IDA Inferred from Direct Assay more info	PubMed
enables cadherin binding	IPI Inferred from Physical Interaction more info	PubMed
enables cholesterol binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in camera-type eye photoreceptor cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in camera-type eye photoreceptor cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in camera-type eye photoreceptor cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in glomerular parietal epithelial cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in photoreceptor cell maintenance	IBA Inferred from Biological aspect of Ancestor more info
involved_in photoreceptor cell maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in podocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of nephron tubule epithelial cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retina layer formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in retina morphogenesis in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in apical plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cell surface	IBA Inferred from Biological aspect of Ancestor more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
is_active_in cilium	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum-Golgi intermediate compartment	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular exosome	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	HDA more info	PubMed
is_active_in microvillus	IBA Inferred from Biological aspect of Ancestor more info
located_in microvillus membrane	IEA Inferred from Electronic Annotation more info
located_in photoreceptor outer segment	ISS Inferred from Sequence or Structural Similarity more info
located_in photoreceptor outer segment membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in prominosome	IBA Inferred from Biological aspect of Ancestor more info
located_in vesicle	HDA more info	PubMed

General protein information

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Preferred Names: prominin-1

Names: AC133 antigen; Retinitis pigmentosa 41, Cone-rod dystrophy 12; antigen AC133; hProminin; hematopoietic stem cell antigen; prominin-like protein 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_011696.2 RefSeqGene

Range

5037..120832

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001145847.2 → NP_001139319.1 prominin-1 isoform 2 precursor

See identical proteins and their annotated locations for NP_001139319.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) represents one of several alternative promoters and 5' UTRs, and lacks an alternative in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (2), also known as s1, lacks a 9 aa segment near the N-terminus, compared to isoform 1. Both variants 2 and 3 encode the same isoform.

Source sequence(s)

AC005598, AC108063

Consensus CDS

CCDS54746.1

UniProtKB/TrEMBL

A0A0A0N0M1, B3KNF4, B3KQS1

Related

ENSP00000427346.1, ENST00000508167.5

Conserved Domains (1) summary

pfam05478
Location:18 → 811

Prominin
NM_001145848.2 → NP_001139320.1 prominin-1 isoform 2 precursor

See identical proteins and their annotated locations for NP_001139320.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents one of several alternative promoters and 5' UTRs, and lacks an alternative in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (2), also known as s1, lacks a 9 aa segment near the N-terminus, compared to isoform 1. Both variants 2 and 3 encode the same isoform.

Source sequence(s)

AC005598, AC108063

Consensus CDS

CCDS54746.1

UniProtKB/TrEMBL

A0A0A0N0M1, B3KNF4, B3KQS1

Related

ENSP00000426090.1, ENST00000505450.5

Conserved Domains (1) summary

pfam05478
Location:18 → 811

Prominin
NM_001145849.2 → NP_001139321.1 prominin-1 isoform 7 precursor

See identical proteins and their annotated locations for NP_001139321.1

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (7), also known as s12, lacks an internal segment near the C-terminus, compared to isoform 1. The full structure of the 5' UTR for this variant has not been determined.

Source sequence(s)

AC005598, AY449693, BC012089

Consensus CDS

CCDS54748.1

UniProtKB/TrEMBL

B3KNF4, B3KQS1

Related

ENSP00000502545.1, ENST00000675377.1

Conserved Domains (1) summary

pfam05478
Location:18 → 820

Prominin; Prominin
NM_001145850.2 → NP_001139322.1 prominin-1 isoform 6 precursor

See identical proteins and their annotated locations for NP_001139322.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks two alternate in-frame exons in the 3' coding region, compared to variant 1. The resulting isoform (6), also known as s11, lacks an internal segment near the C-terminus, compared to isoform 1.

Source sequence(s)

AC005598, AC108063

Consensus CDS

CCDS54747.1

UniProtKB/TrEMBL

B3KNF4, B3KQS1

Related

ENSP00000443620.1, ENST00000539194.6

Conserved Domains (1) summary

pfam05478
Location:18 → 820

Prominin; Prominin
NM_001145851.2 → NP_001139323.1 prominin-1 isoform 5 precursor

See identical proteins and their annotated locations for NP_001139323.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 5' coding region and a second in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (5), also known as s10, lacks an internal segment near the N-terminus and a second internal segment near the C-terminus, compared to isoform 1. The full structure of the 5' UTR for this variant has not been determined.

Source sequence(s)

AC005598, AY449691, BC012089, DB326234

Consensus CDS

CCDS93483.1

UniProtKB/TrEMBL

B3KNF4, B3KQS1

Related

ENSP00000438045.2, ENST00000540805.6

Conserved Domains (1) summary

pfam05478
Location:18 → 811

Prominin; Prominin
NM_001145852.2 → NP_001139324.1 prominin-1 isoform 4 precursor

See identical proteins and their annotated locations for NP_001139324.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region and two in-frame exons in the 3' coding region, compared to variant 1. The resulting isoform (4), also known as s7, lacks an internal segment near the N-terminus and a second internal segment near the C-terminus, compared to isoform 1.

Source sequence(s)

AC005598, AC108063

Consensus CDS

CCDS93482.1

UniProtKB/TrEMBL

B3KNF4, B3KQS1

Conserved Domains (1) summary

pfam05478
Location:18 → 811

Prominin
NM_001371406.1 → NP_001358335.1 prominin-1 isoform 2 precursor

Status: REVIEWED

Source sequence(s)

AC005598, AC108063

Consensus CDS

CCDS54746.1

UniProtKB/TrEMBL

A0A0A0N0M1, B3KNF4, B3KQS1

Conserved Domains (1) summary

pfam05478
Location:18 → 811

Prominin
NM_001371407.1 → NP_001358336.1 prominin-1 isoform 4 precursor

Status: REVIEWED

Source sequence(s)

AC005598, AC108063

Consensus CDS

CCDS93482.1

UniProtKB/TrEMBL

B3KNF4, B3KQS1

Conserved Domains (1) summary

pfam05478
Location:18 → 811

Prominin
NM_001371408.1 → NP_001358337.1 prominin-1 isoform 4 precursor

Status: REVIEWED

Source sequence(s)

AC005598, AC108063

Consensus CDS

CCDS93482.1

UniProtKB/TrEMBL

B3KNF4, B3KQS1

Related

ENSP00000501741.1, ENST00000675613.1

Conserved Domains (1) summary

pfam05478
Location:18 → 811

Prominin
NM_006017.3 → NP_006008.1 prominin-1 isoform 1 precursor

See identical proteins and their annotated locations for NP_006008.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest isoform (1), also known as s2.

Source sequence(s)

AC005598, AC108063

Consensus CDS

CCDS47029.1

UniProtKB/Swiss-Prot

O43490, Q6SV49, Q6SV50, Q6SV51, Q6SV52, Q6SV53, Q96EN6

UniProtKB/TrEMBL

B3KNF4, B3KQS1

Related

ENSP00000415481.2, ENST00000447510.7

Conserved Domains (1) summary

pfam05478
Location:18 → 820

Prominin; Prominin