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RAPH1 Ras association (RalGDS/AF-6) and pleckstrin homology domains 1 [ Homo sapiens (human) ]

Gene ID: 65059, updated on 7-Apr-2024

Summary

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Official Symbol
RAPH1provided by HGNC
Official Full Name
Ras association (RalGDS/AF-6) and pleckstrin homology domains 1provided by HGNC
Primary source
HGNC:HGNC:14436
See related
Ensembl:ENSG00000173166 MIM:609035; AllianceGenome:HGNC:14436
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
LPD; RMO1; PREL2; PREL-2; ALS2CR9; ALS2CR18; RalGDS/AF-6
Summary
This gene encodes a protein that belongs to the Mig10/Rap1-interacting adaptor molecule/Lamellipodin family of adapter proteins, which function in cell migration. Members of this family contain pleckstrin-homology domains, Ras-association domains, and proline-rich C-termini. The protein encoded by this gene regulates actin dynamics through interaction with Ena/Vasodilator proteins as well as direct binding to filamentous actin to regulate actin network assembly. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]
Expression
Ubiquitous expression in thyroid (RPKM 14.2), liver (RPKM 12.2) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
2q33.2
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (203433682..203535301, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (203915590..204017213, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (204298405..204400024, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:204192004-204192974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12255 Neighboring gene mitochondrial ribosomal protein L50 pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:204209822-204210322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17011 Neighboring gene MPRA-validated peak4020 silencer Neighboring gene abl interactor 2 Neighboring gene tRNA-Glu (anticodon TTC) 9-1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12258 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:204464991-204465874 Neighboring gene zinc finger protein 207 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:204530085-204530727 Neighboring gene NDUFA4, mitochondrial complex associated pseudogene

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. Clinicopathological and prognostic significance of Ras association and pleckstrin homology domains 1 (RAPH1) in breast cancer. Kurozumi S, et al. Breast Cancer Res Treat, 2018 Nov. PMID 30056565
  2. Association between RAPH1 Gene Haplotypes and CHE2 Locus Phenotypes. A De Andrade F, et al. Ann Hum Genet, 2016 Jul. PMID 27346732
  3. Mechanistic insights into the phosphatidylinositol binding properties of the pleckstrin homology domain of lamellipodin. Gorai S, et al. Mol Biosyst, 2016 Mar. PMID 26726010
  4. Lamellipodin Is Important for Cell-to-Cell Spread and Actin-Based Motility in Listeria monocytogenes. Wang J, et al. Infect Immun, 2015 Sep. PMID 26169271, Free PMC Article
  5. Amplification and deletion of the RAPH1 gene in breast cancer patients. Batistela MS, et al. Mol Biol Rep, 2013 Dec. PMID 24057252

See all (65) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Nuclear isoform of RAPH1 interacts with FOXQ1 to promote aggressiveness and radioresistance in breast cancer.
    Title: Nuclear isoform of RAPH1 interacts with FOXQ1 to promote aggressiveness and radioresistance in breast cancer.
  2. High RAPH1 expression is correlated with aggressive breast cancer phenotypes and provides independent prognostic value in invasive breast cancer.
    Title: Clinicopathological and prognostic significance of Ras association and pleckstrin homology domains 1 (RAPH1) in breast cancer.
  3. The human RAPH1 gene is the CHE2 locus.
    Title: Association between RAPH1 Gene Haplotypes and CHE2 Locus Phenotypes.
  4. these studies demonstrate an insight into how the Lpd-PH domain regulates cellular signals in a PI(3,4)P2 dependent manner.
    Title: Mechanistic insights into the phosphatidylinositol binding properties of the pleckstrin homology domain of lamellipodin.
  5. Disruption of the RIAM/lamellipodin-integrin-talin complex markedly impairs cell migration.
    Title: A RIAM/lamellipodin-talin-integrin complex forms the tip of sticky fingers that guide cell migration.
  6. The authors propose that Lpd delivers Ena/VASP proteins to growing barbed ends and increases their actin polymerase activity by tethering them to actin filaments.
    Title: Lamellipodin promotes actin assembly by clustering Ena/VASP proteins and tethering them to actin filaments.
  7. These data indicate a possible role for Lpd in the actin-based movement and the cell-to-cell spread of L. monocytogenes.
    Title: Lamellipodin Is Important for Cell-to-Cell Spread and Actin-Based Motility in Listeria monocytogenes.
  8. The results suggest that although the RAPH1 gene was deleted or amplified in all samples, the Lpd does not seem to play a major role in tumorigenesis of mammary carcinomas.
    Title: Amplification and deletion of the RAPH1 gene in breast cancer patients.
  9. this study suggests a novel mechanism in which Lpd mediates EGFR endocytosis via Mena downstream of endophilin.
    Title: Endophilin, Lamellipodin, and Mena cooperate to regulate F-actin-dependent EGF-receptor endocytosis.
  10. The crystal structure of Lpd cc-RA-PH presents a molecular model of Lpd enhances actin polymerization by oligomerization via two intermolecular contact sites.
    Title: Crystal structure of Lamellipodin implicates diverse functions in actin polymerization and Ras signaling.
Submit: New GeneRIF Correction See all GeneRIFs (16)

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

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

Clone Names

  • KIAA1681

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in axon extension IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in filopodium IEA
Inferred from Electronic Annotation
more info
  
located_in lamellipodium IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
ras-associated and pleckstrin homology domains-containing protein 1
Names
amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18
amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9
lamellipodin
proline-rich EVH1 ligand 2

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_001329728.2 → NP_001316657.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC018891
    UniProtKB/TrEMBL
    C9J164
    Conserved Domains (3) summary
    cd01259
    Location:444 → 566
    PH_APBB1IP; Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain
    pfam00169
    Location:449 → 557
    PH; PH domain
    cl00155
    Location:321 → 402
    UBQ; Ubiquitin-like proteins

  2. NM_203365.4 → NP_976241.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform 3

    See identical proteins and their annotated locations for NP_976241.1

    Status: REVIEWED

    Source sequence(s)
    AC018891, AI217860, AY523978, BE967038
    Consensus CDS
    CCDS2360.1
    UniProtKB/TrEMBL
    C9J164
    Related
    ENSP00000311293.4, ENST00000308091.8
    Conserved Domains (3) summary
    cd01259
    Location:444 → 566
    PH_APBB1IP; Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain
    pfam00169
    Location:449 → 557
    PH; PH domain
    cl00155
    Location:321 → 402
    UBQ; Ubiquitin-like proteins

  3. NM_213589.3 → NP_998754.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_998754.1

    Status: REVIEWED

    Source sequence(s)
    AC018891, AI217860, AJ584699, AY494951, CA503229
    Consensus CDS
    CCDS2359.1
    UniProtKB/Swiss-Prot
    Q70E73, Q96Q37, Q9C0I2
    Related
    ENSP00000316543.5, ENST00000319170.10
    Conserved Domains (3) summary
    cd01259
    Location:392 → 514
    PH_APBB1IP; Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain
    pfam00169
    Location:397 → 505
    PH; PH domain
    cl00155
    Location:269 → 350
    UBQ; Ubiquitin-like proteins

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    203433682..203535301 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047445545.1 → XP_047301501.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X6

  2. XM_047445544.1 → XP_047301500.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X5

  3. XM_005246777.5 → XP_005246834.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

    See identical proteins and their annotated locations for XP_005246834.1

    UniProtKB/TrEMBL
    C9K0J5
    Related
    ENSP00000486548.1, ENST00000630330.2
    Conserved Domains (3) summary
    cd01259
    Location:444 → 566
    PH_APBB1IP; Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain
    pfam00169
    Location:449 → 557
    PH; PH domain
    cl00155
    Location:321 → 402
    UBQ; Ubiquitin-like proteins

  4. XM_047445548.1 → XP_047301504.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X8

    UniProtKB/Swiss-Prot
    Q70E73, Q96Q37, Q9C0I2

  5. XM_047445546.1 → XP_047301502.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X6

  6. XM_011511646.4 → XP_011509948.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

    See identical proteins and their annotated locations for XP_011509948.1

    UniProtKB/TrEMBL
    C9K0J5
    Conserved Domains (3) summary
    cd01259
    Location:444 → 566
    PH_APBB1IP; Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain
    pfam00169
    Location:449 → 557
    PH; PH domain
    cl00155
    Location:321 → 402
    UBQ; Ubiquitin-like proteins

  7. XM_047445547.1 → XP_047301503.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X7

  8. XM_047445543.1 → XP_047301499.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X4

  9. XM_047445542.1 → XP_047301498.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X3

  10. XM_047445538.1 → XP_047301494.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X1

  11. XM_047445540.1 → XP_047301496.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    C9K0J5

  12. XM_047445541.1 → XP_047301497.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    C9K0J5

  13. XM_047445539.1 → XP_047301495.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    C9K0J5

  14. XM_006712695.4 → XP_006712758.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

    See identical proteins and their annotated locations for XP_006712758.1

    UniProtKB/TrEMBL
    C9K0J5
    Conserved Domains (3) summary
    cd01259
    Location:444 → 566
    PH_APBB1IP; Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain
    pfam00169
    Location:449 → 557
    PH; PH domain
    cl00155
    Location:321 → 402
    UBQ; Ubiquitin-like proteins

  15. XM_047445549.1 → XP_047301505.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X9

  16. XM_047445551.1 → XP_047301507.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X11

    Related
    ENSP00000411138.1, ENST00000439222.5

  17. XM_047445550.1 → XP_047301506.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X10

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    203915590..204017213 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054343441.1 → XP_054199416.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X6

  2. XM_054343440.1 → XP_054199415.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X5

  3. XM_054343436.1 → XP_054199411.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    C9K0J5

  4. XM_054343443.1 → XP_054199418.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X8

    UniProtKB/Swiss-Prot
    Q70E73, Q96Q37, Q9C0I2

  5. XM_054343442.1 → XP_054199417.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X6

  6. XM_054343437.1 → XP_054199412.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    C9K0J5

  7. XM_054343439.1 → XP_054199414.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    C9K0J5

  8. XM_054343438.1 → XP_054199413.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    C9K0J5

  9. XM_054343444.1 → XP_054199419.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X9

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NG_051287.1: Suppressed sequence

    Description
    NG_051287.1: This RefSeq was removed by NCBI staff. Please email info@ncbi.nlm.nih.gov for more information.

  2. NM_025252.3: Suppressed sequence

    Description
    NM_025252.3: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q70E73.3 GenPept UniProtKB/Swiss-Prot:Q70E73

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