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FREM1 FRAS1 related extracellular matrix 1 [ Homo sapiens (human) ]

Gene ID: 158326, updated on 3-Apr-2024

Summary

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Official Symbol
FREM1provided by HGNC
Official Full Name
FRAS1 related extracellular matrix 1provided by HGNC
Primary source
HGNC:HGNC:23399
See related
Ensembl:ENSG00000164946 MIM:608944; AllianceGenome:HGNC:23399
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
BNAR; MOTA; TILRR; TRIGNO2; C9orf143; C9orf145; C9orf154
Summary
This gene encodes a basement membrane protein that may play a role in craniofacial and renal development. Mutations in this gene have been associated with bifid nose with or without anorectal and renal anomalies. Alternatively spliced transcript variants encoding different isoforms have been described. PubMed ID 19940113 describes one such variant that initiates transcription within a distinct, internal exon; the resulting shorter isoform (named Toll-like/interleukin-1 receptor regulator, TILRR) is suggested to be a co-receptor of the interleukin 1 receptor family and may regulate receptor function and Toll-like receptor/interleukin 1 receptor signal transduction, contributing to the control of inflammatory response activation. [provided by RefSeq, Apr 2011]
Expression
Broad expression in endometrium (RPKM 5.0), kidney (RPKM 2.2) and 14 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
9p22.3
Exon count:
46
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (14737152..14910995, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (14746865..14921449, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (14737150..14910993, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:14597299-14597830 Neighboring gene zinc finger DHHC-type palmitoyltransferase 21 Neighboring gene cell division cycle associated 4 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19776 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:14693435-14693935 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:14721879-14722818 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:14722819-14723756 Neighboring gene cerberus 1, DAN family BMP antagonist Neighboring gene uncharacterized LOC105375979 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:14812530-14813729 Neighboring gene RNA, U6 small nuclear 1260, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:14907200-14907740 Neighboring gene NANOG hESC enhancer GRCh37_chr9:14908690-14909191 Neighboring gene uncharacterized LOC124902122 Neighboring gene lactate dehydrogenase A pseudogene 4

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. High level of plasma TILRR protein is associated with faster HIV seroconversion. Kashem MA, et al. EBioMedicine, 2022 Apr. PMID 35339895, Free PMC Article
  2. Elevated expression of FREM1 in breast cancer indicates favorable prognosis and high-level immune infiltration status. Li HN, et al. Cancer Med, 2020 Dec. PMID 33058542, Free PMC Article
  3. Heterozygous intragenic deletions of FREM1 are not associated with trigonocephaly. Dawson AJ, et al. Clin Dysmorphol, 2021 Apr 1. PMID 33038106
  4. Bifid nose as the sole manifestation of BNAR syndrome, a FREM1-related condition. Brischoux-Boucher E, et al. Clin Genet, 2020 Nov. PMID 32926405
  5. Toll-like Interleukin 1 Receptor Regulator Is an Important Modulator of Inflammation Responsive Genes. Kashem MA, et al. Front Immunol, 2019. PMID 30873160, Free PMC Article

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Two novel mutations within FREM1 gene in patients with bifid nose.
    Title: Two novel mutations within FREM1 gene in patients with bifid nose.
  2. High level of plasma TILRR protein is associated with faster HIV seroconversion.
    Title: High level of plasma TILRR protein is associated with faster HIV seroconversion.
  3. Heterozygous intragenic deletions of FREM1 are not associated with trigonocephaly.
    Title: Heterozygous intragenic deletions of FREM1 are not associated with trigonocephaly.
  4. Bifid nose as the sole manifestation of BNAR syndrome, a FREM1-related condition.
    Title: Bifid nose as the sole manifestation of BNAR syndrome, a FREM1-related condition.
  5. Elevated expression of FREM1 in breast cancer indicates favorable prognosis and high-level immune infiltration status.
    Title: Elevated expression of FREM1 in breast cancer indicates favorable prognosis and high-level immune infiltration status.
  6. Toll-like Interleukin 1 Receptor Regulator Is an Important Modulator of Inflammation Responsive Genes.
    Title: Toll-like Interleukin 1 Receptor Regulator Is an Important Modulator of Inflammation Responsive Genes.
  7. Our results showed that p.Arg2167Trp had a weaker effect in interrupting interactions between FREM2 and FREM1 than FS-associated missense mutation p.Glu1972Lys. Overall, our data demonstrate that the homozygous mutation p.Arg2167Trp in FREM2 causes isolated Cryptophthalmos(CO), which will facilitate our better understanding of the molecular mechanisms underlying the disease
    Title: A homozygous mutation p.Arg2167Trp in FREM2 causes isolated cryptophthalmos.
  8. we identified genome-wide significant association involving measures of central upper lip height at 9p22 within FREM1
    Title: Genome-wide association study of facial morphology reveals novel associations with FREM1 and PARK2.
  9. FREM1 expression is significantly downregulated in human masticatory mucosa during wound healing
    Title: Human gingiva transcriptome during wound healing.
  10. this report describes a patient with a phenotype compatible with Manitoba-oculo-tricho-anal syndrome in whom two novel FREM1 mutations were identified in the compound heterozygous state thus broadening the mutational spectrum of the disease.
    Title: Novel FREM1 mutations in a patient with MOTA syndrome: Clinical findings, mutation update and review of FREM1-related disorders literature.
Submit: New GeneRIF Correction See all GeneRIFs (23)

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
BNAR syndrome
MedGen: C2750433 OMIM: 608980 GeneReviews: FREM1 Autosomal Recessive Disorders
Compare labs
Oculotrichoanal syndrome
MedGen: C1855425 OMIM: 248450 GeneReviews: FREM1 Autosomal Recessive Disorders
Compare labs
Trigonocephaly 2
MedGen: C3280974 OMIM: 614485 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Identification of 15 loci influencing height in a Korean population.
EBI GWAS Catalog

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ25461

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables carbohydrate binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 cell-matrix adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in craniofacial suture morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in basement membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
FRAS1-related extracellular matrix protein 1
Names
extracellular matrix protein QBRICK

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

  1. NG_017005.2 RefSeqGene

    Range
    4809..178085
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001177704.3 → NP_001171175.1  FRAS1-related extracellular matrix protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001171175.1

    Status: REVIEWED

    Source sequence(s)
    AL390732, AL512643
    Consensus CDS
    CCDS55293.1
    UniProtKB/Swiss-Prot
    Q5H8C1
    Related
    ENSP00000370278.1, ENST00000380894.5
    Conserved Domains (3) summary
    smart00034
    Location:589 → 711
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:25 → 134
    Cadherin_3; Cadherin-like
    cl02522
    Location:282 → 365
    Calx-beta; Calx-beta domain

  2. NM_001370058.2 → NP_001356987.1  FRAS1-related extracellular matrix protein 1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL390732, AL512643
    Conserved Domains (1) summary
    cl02522
    Location:282 → 340
    Calx-beta; Calx-beta domain

  3. NM_001370060.1 → NP_001356989.1  FRAS1-related extracellular matrix protein 1 isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AL354672, AL512643
    Conserved Domains (1) summary
    pfam16184
    Location:324 → 400
    Cadherin_3; Cadherin-like

  4. NM_001370061.2 → NP_001356990.1  FRAS1-related extracellular matrix protein 1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL390732, AL512643
    Consensus CDS
    CCDS55293.1
    Conserved Domains (3) summary
    smart00034
    Location:589 → 711
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:25 → 134
    Cadherin_3; Cadherin-like
    cl02522
    Location:282 → 365
    Calx-beta; Calx-beta domain

  5. NM_001370063.1 → NP_001356992.1  FRAS1-related extracellular matrix protein 1 isoform 5 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6), as well as variant 7, encodes isoform 5.
    Source sequence(s)
    AL354672, AL512643
    Conserved Domains (1) summary
    pfam16184
    Location:315 → 391
    Cadherin_3; Cadherin-like

  6. NM_001370065.1 → NP_001356994.1  FRAS1-related extracellular matrix protein 1 isoform 5 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7), as well as variant 6, encodes isoform 5.
    Source sequence(s)
    AL354672, AL512643
    Conserved Domains (1) summary
    pfam16184
    Location:315 → 391
    Cadherin_3; Cadherin-like

  7. NM_001379081.2 → NP_001366010.1  FRAS1-related extracellular matrix protein 1 isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AL354672, AL390732, AL512643
    Consensus CDS
    CCDS47952.1
    UniProtKB/Swiss-Prot
    B7ZBX4, Q5H8C1, Q5VV00, Q5VV01, Q6MZI4, Q8NEG9, Q96LI3
    Related
    ENSP00000370262.3, ENST00000380880.4
    Conserved Domains (3) summary
    smart00034
    Location:2053 → 2175
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:1489 → 1598
    Cadherin_3; Cadherin-like
    cl02522
    Location:1746 → 1829
    Calx-beta; Calx-beta domain

  8. NM_144966.7 → NP_659403.4  FRAS1-related extracellular matrix protein 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_659403.4

    Status: REVIEWED

    Source sequence(s)
    AL354672, AL390732, AL512643
    Consensus CDS
    CCDS47952.1
    UniProtKB/Swiss-Prot
    B7ZBX4, Q5H8C1, Q5VV00, Q5VV01, Q6MZI4, Q8NEG9, Q96LI3
    Conserved Domains (3) summary
    smart00034
    Location:2053 → 2175
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:1489 → 1598
    Cadherin_3; Cadherin-like
    cl02522
    Location:1746 → 1829
    Calx-beta; Calx-beta domain

RNA

  1. NR_163238.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL354672, AL390732, AL512643
    Related
    ENST00000380875.7

  2. NR_163239.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL354672, AL390732, AL512643

  3. NR_163240.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL354672, AL512643

  4. NR_163241.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL354672, AL512643

  5. NR_163242.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL390732, AL512643

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    14737152..14910995 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422844.1 → XP_047278800.1  FRAS1-related extracellular matrix protein 1 isoform X1

  2. XM_047422847.1 → XP_047278803.1  FRAS1-related extracellular matrix protein 1 isoform X2

    UniProtKB/Swiss-Prot
    B7ZBX4, Q5H8C1, Q5VV00, Q5VV01, Q6MZI4, Q8NEG9, Q96LI3

  3. XM_017014322.2 → XP_016869811.1  FRAS1-related extracellular matrix protein 1 isoform X1

  4. XM_047422846.1 → XP_047278802.1  FRAS1-related extracellular matrix protein 1 isoform X2

    UniProtKB/Swiss-Prot
    B7ZBX4, Q5H8C1, Q5VV00, Q5VV01, Q6MZI4, Q8NEG9, Q96LI3

  5. XM_017014321.3 → XP_016869810.1  FRAS1-related extracellular matrix protein 1 isoform X1

  6. XM_017014324.3 → XP_016869813.1  FRAS1-related extracellular matrix protein 1 isoform X3

  7. XM_017014325.3 → XP_016869814.1  FRAS1-related extracellular matrix protein 1 isoform X4

  8. XM_017014316.3 → XP_016869805.1  FRAS1-related extracellular matrix protein 1 isoform X1

  9. XM_047422848.1 → XP_047278804.1  FRAS1-related extracellular matrix protein 1 isoform X2

    UniProtKB/Swiss-Prot
    B7ZBX4, Q5H8C1, Q5VV00, Q5VV01, Q6MZI4, Q8NEG9, Q96LI3

  10. XM_017014320.3 → XP_016869809.1  FRAS1-related extracellular matrix protein 1 isoform X1

  11. XM_017014319.3 → XP_016869808.1  FRAS1-related extracellular matrix protein 1 isoform X1

  12. XM_047422845.1 → XP_047278801.1  FRAS1-related extracellular matrix protein 1 isoform X1

  13. XM_017014326.2 → XP_016869815.1  FRAS1-related extracellular matrix protein 1 isoform X5

  14. XM_017014327.3 → XP_016869816.1  FRAS1-related extracellular matrix protein 1 isoform X6

  15. XM_006716729.4 → XP_006716792.1  FRAS1-related extracellular matrix protein 1 isoform X19

    See identical proteins and their annotated locations for XP_006716792.1

    UniProtKB/Swiss-Prot
    Q5H8C1
    Conserved Domains (3) summary
    smart00034
    Location:589 → 711
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:25 → 134
    Cadherin_3; Cadherin-like
    cl02522
    Location:282 → 365
    Calx-beta; Calx-beta domain

  16. XM_047422859.1 → XP_047278815.1  FRAS1-related extracellular matrix protein 1 isoform X20

  17. XM_011517758.3 → XP_011516060.1  FRAS1-related extracellular matrix protein 1 isoform X18

    Conserved Domains (3) summary
    smart00034
    Location:601 → 723
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:115 → 273
    Cadherin_3; Cadherin-like
    cl02522
    Location:294 → 377
    Calx-beta; Calx-beta domain

  18. XM_017014329.3 → XP_016869818.1  FRAS1-related extracellular matrix protein 1 isoform X8

  19. XM_017014328.3 → XP_016869817.1  FRAS1-related extracellular matrix protein 1 isoform X7

  20. XM_047422852.1 → XP_047278808.1  FRAS1-related extracellular matrix protein 1 isoform X12

  21. XM_047422851.1 → XP_047278807.1  FRAS1-related extracellular matrix protein 1 isoform X11

  22. XM_047422850.1 → XP_047278806.1  FRAS1-related extracellular matrix protein 1 isoform X10

  23. XM_047422849.1 → XP_047278805.1  FRAS1-related extracellular matrix protein 1 isoform X9

  24. XM_047422854.1 → XP_047278810.1  FRAS1-related extracellular matrix protein 1 isoform X14

  25. XM_047422853.1 → XP_047278809.1  FRAS1-related extracellular matrix protein 1 isoform X13

  26. XM_047422858.1 → XP_047278814.1  FRAS1-related extracellular matrix protein 1 isoform X17

  27. XM_047422857.1 → XP_047278813.1  FRAS1-related extracellular matrix protein 1 isoform X17

  28. XM_047422856.1 → XP_047278812.1  FRAS1-related extracellular matrix protein 1 isoform X17

  29. XM_047422855.1 → XP_047278811.1  FRAS1-related extracellular matrix protein 1 isoform X15

  30. XM_017014330.3 → XP_016869819.1  FRAS1-related extracellular matrix protein 1 isoform X16

    UniProtKB/TrEMBL
    F8WE85

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    14746865..14921449 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362116.1 → XP_054218091.1  FRAS1-related extracellular matrix protein 1 isoform X1

  2. XM_054362110.1 → XP_054218085.1  FRAS1-related extracellular matrix protein 1 isoform X1

  3. XM_054362111.1 → XP_054218086.1  FRAS1-related extracellular matrix protein 1 isoform X1

  4. XM_054362115.1 → XP_054218090.1  FRAS1-related extracellular matrix protein 1 isoform X1

  5. XM_054362118.1 → XP_054218093.1  FRAS1-related extracellular matrix protein 1 isoform X2

  6. XM_054362117.1 → XP_054218092.1  FRAS1-related extracellular matrix protein 1 isoform X2

  7. XM_054362114.1 → XP_054218089.1  FRAS1-related extracellular matrix protein 1 isoform X1

  8. XM_054362120.1 → XP_054218095.1  FRAS1-related extracellular matrix protein 1 isoform X3

  9. XM_054362121.1 → XP_054218096.1  FRAS1-related extracellular matrix protein 1 isoform X4

  10. XM_054362109.1 → XP_054218084.1  FRAS1-related extracellular matrix protein 1 isoform X1

  11. XM_054362119.1 → XP_054218094.1  FRAS1-related extracellular matrix protein 1 isoform X2

  12. XM_054362113.1 → XP_054218088.1  FRAS1-related extracellular matrix protein 1 isoform X1

  13. XM_054362112.1 → XP_054218087.1  FRAS1-related extracellular matrix protein 1 isoform X1

  14. XM_054362122.1 → XP_054218097.1  FRAS1-related extracellular matrix protein 1 isoform X5

  15. XM_054362123.1 → XP_054218098.1  FRAS1-related extracellular matrix protein 1 isoform X6

  16. XM_054362138.1 → XP_054218113.1  FRAS1-related extracellular matrix protein 1 isoform X19

  17. XM_054362139.1 → XP_054218114.1  FRAS1-related extracellular matrix protein 1 isoform X20

  18. XM_054362137.1 → XP_054218112.1  FRAS1-related extracellular matrix protein 1 isoform X18

  19. XM_054362125.1 → XP_054218100.1  FRAS1-related extracellular matrix protein 1 isoform X8

  20. XM_054362124.1 → XP_054218099.1  FRAS1-related extracellular matrix protein 1 isoform X7

  21. XM_054362129.1 → XP_054218104.1  FRAS1-related extracellular matrix protein 1 isoform X12

  22. XM_054362128.1 → XP_054218103.1  FRAS1-related extracellular matrix protein 1 isoform X11

  23. XM_054362127.1 → XP_054218102.1  FRAS1-related extracellular matrix protein 1 isoform X10

  24. XM_054362126.1 → XP_054218101.1  FRAS1-related extracellular matrix protein 1 isoform X9

  25. XM_054362131.1 → XP_054218106.1  FRAS1-related extracellular matrix protein 1 isoform X14

  26. XM_054362130.1 → XP_054218105.1  FRAS1-related extracellular matrix protein 1 isoform X13

  27. XM_054362136.1 → XP_054218111.1  FRAS1-related extracellular matrix protein 1 isoform X17

  28. XM_054362135.1 → XP_054218110.1  FRAS1-related extracellular matrix protein 1 isoform X17

  29. XM_054362134.1 → XP_054218109.1  FRAS1-related extracellular matrix protein 1 isoform X17

  30. XM_054362132.1 → XP_054218107.1  FRAS1-related extracellular matrix protein 1 isoform X15

  31. XM_054362133.1 → XP_054218108.1  FRAS1-related extracellular matrix protein 1 isoform X16

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5H8C1.3 GenPept UniProtKB/Swiss-Prot:Q5H8C1

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