U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

FRAS1 Fraser extracellular matrix complex subunit 1 [ Homo sapiens (human) ]

Gene ID: 80144, updated on 5-Mar-2024

Summary

Go to the top of the page Help
Official Symbol
FRAS1provided by HGNC
Official Full Name
Fraser extracellular matrix complex subunit 1provided by HGNC
Primary source
HGNC:HGNC:19185
See related
Ensembl:ENSG00000138759 MIM:607830; AllianceGenome:HGNC:19185
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
FRASRS1
Summary
This gene encodes an extracellular matrix protein that appears to function in the regulation of epidermal-basement membrane adhesion and organogenesis during development. Mutations in this gene cause Fraser syndrome, a multisystem malformation that can include craniofacial, urogenital and respiratory system abnormalities. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
Expression
Broad expression in thyroid (RPKM 6.8), kidney (RPKM 4.0) and 15 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
4q21.21
Exon count:
74
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (78057323..78544269)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (81398139..81879833)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (78978477..79465423)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:78904281-78905096 Neighboring gene high mobility group box 1 pseudogene 44 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 56 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:78977063-78978034 Neighboring gene uncharacterized LOC107986293 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:79013872-79014616 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:79026548-79027162 Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene 5 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:79143534-79144418 Neighboring gene Sharpr-MPRA regulatory region 11576 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:79228222-79228817 Neighboring gene small nucleolar RNA, C/D box 161 Neighboring gene MICOS10 pseudogene 4 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:79402250-79403449 Neighboring gene Sharpr-MPRA regulatory region 1185 Neighboring gene Sharpr-MPRA regulatory region 14158 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:79455131-79456330 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:79473344-79474543 Neighboring gene uncharacterized LOC124900721 Neighboring gene annexin A3

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. A polymorphism in the promoter of FRAS1 is a candidate SNP associated with metastatic prostate cancer. Wang V, et al. Prostate, 2021 Jul. PMID 33956343, Free PMC Article
  2. Two unrelated families with variable expression of Fraser syndrome due to the same pathogenic variant in the FRAS1 gene. Midro AT, et al. Am J Med Genet A, 2020 Apr. PMID 31999076
  3. Fraser extracellular matrix complex subunit 1 promotes liver metastasis of gastric cancer. Umeda S, et al. Int J Cancer, 2020 May 15. PMID 31597194
  4. Expanding the mutation spectrum for Fraser syndrome: identification of a novel heterozygous deletion in FRAS1. Hoefele J, et al. Gene, 2013 May 15. PMID 23473829
  5. Clinical and molecular studies in two families with Fraser syndrome: a new FRAS1 gene mutation, prenatal ultrasound findings and implications for genetic counselling. Ogur G, et al. Genet Couns, 2011. PMID 22029163

See all (47) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A polymorphism in the promoter of FRAS1 is a candidate SNP associated with metastatic prostate cancer.
    Title: A polymorphism in the promoter of FRAS1 is a candidate SNP associated with metastatic prostate cancer.
  2. Novel loss of function variants in FRAS1 AND FREM2 underlie renal agenesis in consanguineous families.
    Title: Novel loss of function variants in FRAS1 AND FREM2 underlie renal agenesis in consanguineous families.
  3. Two unrelated families with variable expression of Fraser syndrome due to the same pathogenic variant in the FRAS1 gene.
    Title: Two unrelated families with variable expression of Fraser syndrome due to the same pathogenic variant in the FRAS1 gene.
  4. Fraser extracellular matrix complex subunit 1 promotes liver metastasis of gastric cancer.
    Title: Fraser extracellular matrix complex subunit 1 promotes liver metastasis of gastric cancer.
  5. Based on these data, we conclude that deficiency of FREM2, and possibly FRAS1, are associated with an increased risk of developing Congenital diaphragmatic hernia (CDH) and that loss of the FREM1/FREM2/FRAS1 complex, or its function, leads to anterior sac CDH development through its effects on mesothelial fold progression
    Title: The role of FREM2 and FRAS1 in the development of congenital diaphragmatic hernia.
  6. In 15 of 590 families, we identified recessive mutations in the genes FRAS1, FREM2, GRIP1, FREM1, ITGA8, and GREM1, all of which function in the interaction of the ureteric bud and the metanephric mesenchyme.
    Title: Mild recessive mutations in six Fraser syndrome-related genes cause isolated congenital anomalies of the kidney and urinary tract.
  7. Analysis of FRAS1 and STRA6 mutations in the same family with eye anomalies.
    Title: A puzzle over several decades: eye anomalies with FRAS1 and STRA6 mutations in the same family.
  8. First case of a family with two patients affected by Fraser syndrome due to a deletion of 64 kb (deletion 4q21.21) and an additional novel frameshift mutation in exon 66 of the FRAS1 gene.
    Title: Expanding the mutation spectrum for Fraser syndrome: identification of a novel heterozygous deletion in FRAS1.
  9. Heterozygous missense mutations in FRAS1 cause non-syndromic congenital abnormalities of the kidney and urinary tract in humans.
    Title: Identification of two novel CAKUT-causing genes by massively parallel exon resequencing of candidate genes in patients with unilateral renal agenesis.
  10. molecular, clinical findings of 4 fetuses with Fraser syndrome from 2 families; in family one, found nonsense mutation (c.3730C>T, p.R1244X) previously described; in family 2 found a novel nonsense mutation previously not known (c.370C>T, p.R124X)
    Title: Clinical and molecular studies in two families with Fraser syndrome: a new FRAS1 gene mutation, prenatal ultrasound findings and implications for genetic counselling.
Submit: New GeneRIF Correction See all GeneRIFs (15)

Phenotypes

Go to the top of the page Help

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
Fraser syndrome 1
MedGen: C4551480 OMIM: 219000 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
A genome wide association study of plasma uric acid levels in obese cases and never-overweight controls.
EBI GWAS Catalog
Common variants in the trichohyalin gene are associated with straight hair in Europeans.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • FLJ14927, FLJ22031, KIAA1500, DKFZp686I05113, DKFZp686P08111

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in anatomical structure morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell communication IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic limb morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in metanephros morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in morphogenesis of an epithelium IEA
Inferred from Electronic Annotation
more info
  
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in roof of mouth development IEA
Inferred from Electronic Annotation
more info
  
involved_in skin development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in basement membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

Go to the top of the page Help
Preferred Names
extracellular matrix organizing protein FRAS1
Names
Fraser syndrome 1
extracellular matrix protein FRAS1
fraser syndrome 1 protein

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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

  1. NG_015812.2 RefSeqGene

    Range
    4754..491700
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001166133.2 → NP_001159605.1  extracellular matrix organizing protein FRAS1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001159605.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the presence and absence of exons in its 3' coding region and 3' UTR, compared to variant 1, resulting in an isoform (2) with a distinct and significantly shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AC093652, AC093886, AK025684, BC131820, DA725113, DA881824
    Consensus CDS
    CCDS54772.1
    UniProtKB/TrEMBL
    A0A804HI32
    Related
    ENSP00000326330.6, ENST00000325942.11
    Conserved Domains (8) summary
    smart00214
    Location:367 → 416
    VWC; von Willebrand factor (vWF) type C domain
    smart00261
    Location:952 → 996
    FU; Furin-like repeats
    cd00064
    Location:608 → 653
    FU; Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
    pfam00093
    Location:95 → 152
    VWC; von Willebrand factor type C domain
    pfam14843
    Location:512 → 623
    GF_recep_IV; Growth factor receptor domain IV
    pfam15913
    Location:1009 → 1099
    Furin-like_2; Furin-like repeat, cysteine-rich
    pfam16184
    Location:1168 → 1310
    Cadherin_3; Cadherin-like
    cl17735
    Location:159 → 216
    VWC; von Willebrand factor type C domain

  2. NM_025074.7 → NP_079350.5  extracellular matrix organizing protein FRAS1 isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB040933, AC093652, AC093886, AC104808, BC131820, BX647420, BX647949, DA725113, DA881824
    Consensus CDS
    CCDS54771.1
    UniProtKB/Swiss-Prot
    A2RRR8, Q86UZ4, Q86XX4, Q8N3U9, Q8NAU7, Q96JW7, Q9H6N9, Q9P228
    Related
    ENSP00000422834.2, ENST00000512123.4
    Conserved Domains (10) summary
    smart00237
    Location:2555 → 2650
    Calx_beta; Domains in Na-Ca exchangers and integrin-beta4
    smart00214
    Location:367 → 416
    VWC; von Willebrand factor (vWF) type C domain
    smart00261
    Location:952 → 996
    FU; Furin-like repeats
    cd00064
    Location:608 → 653
    FU; Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
    pfam00093
    Location:95 → 152
    VWC; von Willebrand factor type C domain
    pfam00757
    Location:462 → 620
    Furin-like; Furin-like cysteine rich region
    pfam14843
    Location:655 → 777
    GF_recep_IV; Growth factor receptor domain IV
    pfam15913
    Location:1009 → 1099
    Furin-like_2; Furin-like repeat, cysteine-rich
    pfam16184
    Location:2261 → 2406
    Cadherin_3; Cadherin-like
    cl02522
    Location:2798 → 2894
    Calx-beta; Calx-beta domain

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    78057323..78544269
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    81398139..81879833
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_020875.1: Suppressed sequence

    Description
    NM_020875.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

  2. NM_032863.2: Suppressed sequence

    Description
    NM_032863.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

  3. NM_206841.1: Suppressed sequence

    Description
    NM_206841.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86XX4.2 GenPept UniProtKB/Swiss-Prot:Q86XX4

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Medical
Molecular Biology Databases
Research Materials
Tools
Miscellaneous