FREM1 (FRAS1 related extracellular matrix 1)

Gene

• Entrez ID: 158326
• Gene name: FRAS1 related extracellular matrix 1
• Gene symbol: FREM1
• Synonyms: BNAR, C9orf143, C9orf145, C9orf154, MOTA, TILRR, TRIGNO2
• Chromosome: 9
• Chromosome location: 9p22.3
• 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs61745612	C>G	Likely-benign, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs121912609	G>A	Pathogenic, not-provided	Genic downstream transcript variant, non coding transcript variant, genic upstream transcript variant, coding sequence variant, missense variant
rs121912610	C>T	Pathogenic, not-provided	Genic downstream transcript variant, non coding transcript variant, downstream transcript variant, genic upstream transcript variant, 5 prime UTR variant, intron variant, coding sequence variant, missense variant
rs184394424	C>G,T	Benign, uncertain-significance, likely-benign, pathogenic	Coding sequence variant, non coding transcript variant, genic upstream transcript variant, genic downstream transcript variant, missense variant
rs281875280	T>A,C	Pathogenic, not-provided	Missense variant, coding sequence variant, genic downstream transcript variant, intron variant, downstream transcript variant, non coding transcript variant
rs370556388	C>G,T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, genic upstream transcript variant, upstream transcript variant, non coding transcript variant
rs373880888	G>A,T	Pathogenic	Synonymous variant, stop gained, coding sequence variant, intron variant, genic downstream transcript variant, non coding transcript variant
rs769407804	AATT>-	Pathogenic	Coding sequence variant, non coding transcript variant, genic downstream transcript variant, genic upstream transcript variant, frameshift variant
rs774044026	G>A	Likely-pathogenic	Upstream transcript variant, coding sequence variant, non coding transcript variant, stop gained, genic upstream transcript variant
rs1064797351	C>A,G,T	Likely-pathogenic	Genic downstream transcript variant, intron variant, splice acceptor variant
rs1588131370	C>-	Pathogenic	Genic upstream transcript variant, frameshift variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT017119	hsa-miR-335-5p	Microarray	18185580
MIRT644905	hsa-miR-186-3p	HITS-CLIP	23824327
MIRT644904	hsa-miR-138-1-3p	HITS-CLIP	23824327
MIRT644903	hsa-miR-5571-3p	HITS-CLIP	23824327
MIRT644902	hsa-miR-7975	HITS-CLIP	23824327
MIRT644901	hsa-miR-384	HITS-CLIP	23824327
MIRT644905	hsa-miR-186-3p	HITS-CLIP	23824327
MIRT644904	hsa-miR-138-1-3p	HITS-CLIP	23824327
MIRT644903	hsa-miR-5571-3p	HITS-CLIP	23824327
MIRT644902	hsa-miR-7975	HITS-CLIP	23824327
MIRT644901	hsa-miR-384	HITS-CLIP	23824327
MIRT1004153	hsa-miR-4490	CLIP-seq
MIRT1004154	hsa-miR-4772-3p	CLIP-seq
MIRT1004155	hsa-miR-4774-5p	CLIP-seq
MIRT1004156	hsa-miR-1179	CLIP-seq
MIRT1004157	hsa-miR-1257	CLIP-seq
MIRT1004158	hsa-miR-1914	CLIP-seq
MIRT1004159	hsa-miR-3121-3p	CLIP-seq
MIRT1004160	hsa-miR-3125	CLIP-seq
MIRT1004161	hsa-miR-338-5p	CLIP-seq
MIRT1004162	hsa-miR-3657	CLIP-seq
MIRT1004163	hsa-miR-3916	CLIP-seq
MIRT1004164	hsa-miR-3928	CLIP-seq
MIRT1004165	hsa-miR-4263	CLIP-seq
MIRT1004166	hsa-miR-4264	CLIP-seq
MIRT1004167	hsa-miR-4276	CLIP-seq
MIRT1004168	hsa-miR-4504	CLIP-seq
MIRT1004169	hsa-miR-4670-3p	CLIP-seq
MIRT1004170	hsa-miR-4720-3p	CLIP-seq
MIRT1004171	hsa-miR-4733-5p	CLIP-seq
MIRT1004172	hsa-miR-4735-5p	CLIP-seq
MIRT1004173	hsa-miR-4781-3p	CLIP-seq
MIRT1004174	hsa-miR-4797-3p	CLIP-seq
MIRT1004175	hsa-miR-4804-3p	CLIP-seq
MIRT1004176	hsa-miR-487a	CLIP-seq
MIRT1004177	hsa-miR-576-5p	CLIP-seq
MIRT1004178	hsa-miR-578	CLIP-seq
MIRT1004179	hsa-miR-643	CLIP-seq
MIRT1997638	hsa-miR-1200	CLIP-seq
MIRT1997639	hsa-miR-216a	CLIP-seq
MIRT1997640	hsa-miR-216b	CLIP-seq
MIRT1997641	hsa-miR-2861	CLIP-seq
MIRT1997642	hsa-miR-3074-5p	CLIP-seq
MIRT1997643	hsa-miR-4324	CLIP-seq
MIRT1997644	hsa-miR-4436a	CLIP-seq
MIRT1997645	hsa-miR-544b	CLIP-seq
MIRT2231322	hsa-miR-1256	CLIP-seq
MIRT1997639	hsa-miR-216a	CLIP-seq
MIRT1997640	hsa-miR-216b	CLIP-seq
MIRT2231323	hsa-miR-217	CLIP-seq
MIRT2231324	hsa-miR-2276	CLIP-seq
MIRT2231325	hsa-miR-23a	CLIP-seq
MIRT2231326	hsa-miR-23b	CLIP-seq
MIRT2231327	hsa-miR-23c	CLIP-seq
MIRT2231328	hsa-miR-3065-3p	CLIP-seq
MIRT2231329	hsa-miR-4283	CLIP-seq
MIRT2231330	hsa-miR-4418	CLIP-seq
MIRT2231331	hsa-miR-4696	CLIP-seq
MIRT1004154	hsa-miR-4772-3p	CLIP-seq
MIRT2231332	hsa-miR-4795-3p	CLIP-seq
MIRT2231333	hsa-miR-4798-5p	CLIP-seq
MIRT2231334	hsa-miR-509-3-5p	CLIP-seq
MIRT2231335	hsa-miR-509-5p	CLIP-seq
MIRT2231336	hsa-miR-587	CLIP-seq
MIRT2231337	hsa-miR-760	CLIP-seq
MIRT2449901	hsa-miR-298	CLIP-seq
MIRT2449902	hsa-miR-29a	CLIP-seq
MIRT2449903	hsa-miR-29b	CLIP-seq
MIRT2449904	hsa-miR-29c	CLIP-seq
MIRT2231328	hsa-miR-3065-3p	CLIP-seq
MIRT2449905	hsa-miR-3678-3p	CLIP-seq
MIRT2535280	hsa-miR-1260	CLIP-seq
MIRT2535281	hsa-miR-1260b	CLIP-seq
MIRT2535282	hsa-miR-188-3p	CLIP-seq
MIRT2535283	hsa-miR-3156-3p	CLIP-seq
MIRT2535284	hsa-miR-3667-3p	CLIP-seq
MIRT2535285	hsa-miR-4301	CLIP-seq
MIRT2535286	hsa-miR-4699-5p	CLIP-seq
MIRT2535287	hsa-miR-548u	CLIP-seq
MIRT2535280	hsa-miR-1260	CLIP-seq
MIRT2535281	hsa-miR-1260b	CLIP-seq
MIRT2535282	hsa-miR-188-3p	CLIP-seq
MIRT2535283	hsa-miR-3156-3p	CLIP-seq
MIRT2535284	hsa-miR-3667-3p	CLIP-seq
MIRT2535285	hsa-miR-4301	CLIP-seq
MIRT2535286	hsa-miR-4699-5p	CLIP-seq
MIRT2535287	hsa-miR-548u	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	29688405
GO:0005604	Component	Basement membrane	IEA
GO:0007154	Process	Cell communication	IEA
GO:0007160	Process	Cell-matrix adhesion	IEA
GO:0016021	Component	Integral component of membrane	IEA
GO:0030246	Function	Carbohydrate binding	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0097094	Process	Craniofacial suture morphogenesis	IMP	21931569

Other IDs

• MIM: 608944
• HGNC: 23399
• e!Ensembl: ENSG00000164946

Protein

• UniProt ID: Q5H8C1
• Protein name: FRAS1-related extracellular matrix protein 1 (Protein QBRICK)
• Protein function: Extracellular matrix protein that plays a role in epidermal differentiation and is required for epidermal adhesion during embryonic development.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF16184	Cadherin_3	292 → 391		Domain
  PF16184	Cadherin_3	396 → 502		Domain
  PF16184	Cadherin_3	504 → 617		Domain
  PF16184	Cadherin_3	623 → 756		Domain
  PF16184	Cadherin_3	760 → 869		Domain
  PF16184	Cadherin_3	871 → 984		Domain
  PF16184	Cadherin_3	1009 → 1128		Domain
  PF16184	Cadherin_3	1131 → 1256		Domain
  PF16184	Cadherin_3	1258 → 1374		Domain
  PF16184	Cadherin_3	1377 → 1487		Domain
  PF16184	Cadherin_3	1489 → 1598		Domain
  PF16184	Cadherin_3	1611 → 1726		Domain
  PF03160	Calx-beta	1731 → 1830	Calx-beta domain	Domain
  PF00059	Lectin_C	2071 → 2177	Lectin C-type domain	Domain

• Sequence:

  MNSLSWGAANAVLLLLLLAWASPTFISINRGVRVMKGHSAFLSGDDLKFAIPKEKDACKV
  EVVMNEPITQRVGKLTPQVFDCHFLPNEVKYVHNGCPILDEDTVKLRLYRFTERDTFIET
  FILWVYLLEPDCNIIHMSNNVLEVPEFNGLSQAIDKNLLRFDYDRMASLECTVSLDTART
  RLPAHGQMVLGEPRPEEPRGDQPHSFFPESQLRAKLKCPGGSCTPGLKKIGSLKVSCEEF
  LLMGLRYQHLDPPSPNIDYISIQLDLTDTRSKIVYKSESAWLPVYIRAGIPNQIPKAAFM
  AVFILEVDQFILTSLTTSVLDCEEDETPKPLLVFNITKAPLQGYVTHLLDHTRPISSFTW
  KDLSDMQIAYQPPNSSHSERRHDEVELEVYDFFFERSAPMTVHISIRTADTNAPRVSWNT
  GLSLLEGQSRAITWEQFQVVDNDDIGAVRLVTVGGLQHGWLTLRGGKGFLFTVADLQAGV
  VRYHHDDSDSTKDFVVFRIFDGHHSIRHKFPINVLPKDDSPPFLITNVVIELEEGQTILI
  QGSMLRASDVDASDDYIFFNITKPPQAGEIMKKPGPGLIGYPVHGFLQRDLFNGIIYYRH
  FGGEIFEDSFQFVLWDSHEPPNLSVPQVATIHITPVDDQLPKEAPGVSRHLVVKETEVAY
  ITKKQLHFIDSESYDRELVYTITTPPFFSFSHRHLDAGKLFMVDSIPKVVKNPTALELRS
  FTQHAVNYMKVAYMPPMQDIGPHCRDVQFTFSVSNQHGGTLHGICFNITILPVDNQVPEA
  FTNPLKVTEGGQSIISTEHILISDADTKLDNIDLSLRELPLHGRVELNGFPLNSGGTFSW
  GDLHTLKVRYQHDGTEVLQDDLLLEVTDGTNSAEFVLHVEVFPVNDEPPVLKADLMPVMN
  CSEGGEVVITSEYIFATDVDSDNLKLMFVIAREPQHGVVRRAGVTVDQFSQRDVISEAVT
  YKHTGGEIGLMPCFDTITLVVSDGEAGPFVNGCCYNGPNPSVPLHASFPVYDLNITVYPV
  DNQPPSIAIGPVFVVDEGCSTALTVNHLSATDPDTAADDLEFVLVSPPQFGYLENILPSV
  GFEKSNIGISIDSFQWKDMNAFHINYVQSRHLRIEPTADQFTVYVTDGKHHSLEIPFSII
  INPTNDEAPDFVVQNITVCEGQMKELDSSIISAVDLDIPQDALLFSITQKPRHGLLIDRG
  FSKDFSENKQPANPHQKHAPVHSFSMELLKTGMRLTYMHDDSESLADDFTIQLSDGKHKI
  LKTISVEVIPVNDEKPMLSKKAEIAMNMGETRIISSAILSAIDEDSPREKIYYVFERLPQ
  NGQLQLKIGRDWVPLSPGMKCTQEEVDLNLLRYTHTGAMDSQNQDSFTFYLWDGNNRSPA
  LDCQITIKDMEKGDIVILTKPLVVSKGDRGFLTTTTLLAVDGTDKPEELLYVITSPPRYG
  QIEYVHYPGVPITNFSQMDVVGQTVCYVHKSKVTVSSDRFRFIISNGLRTEHGVFEITLE
  TVDRALPVVTRNKGLRLAQGAVGLLSPDLLQLTDPDTPAENLTFLLVQLPQHGQLYLWGT
  GLLQHNFTQQDVDSKNVAYRHSGGDSQTDCFTFMATDGTNQGFIVNGRVWEEPVLFTIQV
  DQLDKTAPRITLLHSPSQVGLLKNGCYGIYITSRVLKASDPDTEDDQIIFKILQGPKHGH
  LENTTTGEFIHEKFSQKDLNSKTILYIINPSLEVNSDTVEFQIMDPTGNSATPQILELKW
  SHIEWSQTEYEVCENVGLLPLEIIRRGYSMDSAFVGIKVNQVSAAVGKDFTVIPSKLIQF
  DPGMSTKMWNIAITYDGLEEDDEVFEVILNSPVNAVLGTKTKAAVKILDSKGGQCHPSYS
  SNQSKHSTWEKGIWHLLPPGSSSSTTSGSFHLERRPLPSSMQLAVIRGDTLRGFDSTDLS
  QRKLRTRGNGKTVRPSSVYRNGTDIIYNYHGIVSLKLEDDSFPTHKRKAKVSIISQPQKT
  IKVAELPQADKVESTTDSHFPRQDQLPSFPKNCTLELKGLFHFEEGIQKLYQCNGIAWKA
  WSPQTKDVEDKSCPAGWHQHSGYCHILITEQKGTWNAAAQACREQYLGNLVTVFSRQHMR
  WLWDIGGRKSFWIGLNDQVHAGHWEWIGGEPVAFTNGRRGPSQRSKLGKSCVLVQRQGKW
  QTKDCRRAKPHNYVCSRKL

• Sequence length: 2179

Pathways

KEGG:

ECM-receptor interaction

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Bnar syndrome	BNAR syndrome	rs1588131370
Congenital diaphragmatic hernia	Congenital diaphragmatic hernia	rs121908602, rs121908604, rs864309713, rs780263938, rs756636036, rs775394591	26382659, 23221805
Craniosynostosis	Craniosynostosis, Craniosynostosis, Type 1	rs104893895, rs587777006, rs587777007, rs587777008, rs587777010, rs281865153, rs281865154, rs864321680, rs864321681, rs1057517670, rs1085307122, rs1064794325, rs1884302, rs1555750816, rs1599823350
Microphthalmos	Microphthalmos	rs794726862, rs1329285216
Oculotrichoanal syndrome	Oculotrichoanal syndrome	rs1588131370, rs769407804, rs281875281, rs281875282
Syndromic microphthalmia	Anophthalmos	rs786205873, rs104894464, rs786205874, rs104894465, rs387906701, rs1566623121, rs786205879, rs1566624472, rs397514463, rs1566623392, rs387907252, rs397518481, rs397518482, rs397518483, rs587776457, rs786205884, rs786205224, rs869025222, rs869025221, rs886037853, rs755000701, rs1243762658, rs1555350223, rs1555350156, rs1553637470, rs1566622571, rs1603289774, rs1603289772, rs1579099615, rs1594952111, rs1575553528, rs1575553547, rs1594952007, rs1701696937

Unknown
Disease name	Disease term	dbSNP ID	References
Acrocephaly	Acrocephaly
Bifid nose with or without anorectal and renal anomalies	Bifid Nose With Or Without Anorectal And Renal Anomalies		19732862, 24700879, 11332973, 23401257, 23221805
Brachycephaly	Brachycephaly
Cardiovascular diseases	Cardiovascular Diseases		30595370
Posterolateral diaphragmatic hernia	Congenital hernia of foramen of Bochdalek		26382659, 23221805
Morgagni diaphragmatic hernia	Congenital hernia of foramen of Morgagni		23221805, 26382659
Congenital omphalocele	Congenital omphalocele
Cryptophthalmos	Cryptophthalmos
Disorder of eye	Disorder of eye
Marles greenberg persaud syndrome	Marles Greenberg Persaud syndrome		23112756, 28111185, 11332973, 21507892, 23221805, 17352387
Metopic synostosis	Metopic synostosis
Multicystic renal dysplasia	Congenital anomaly of the kidney
Renal agenesis	Congenital absence of kidneys syndrome, Renal agenesis, unilateral		23221805
Renal aplasia	Unilateral agenesis of kidney		20807610, 24370773
Scaphocephaly	Scaphycephaly
Synophrys	Synophrys
Synostotic anterior plagiocephaly	Synostotic Anterior Plagiocephaly
Synostotic posterior plagiocephaly	Synostotic Posterior Plagiocephaly
Trigonocephaly	Trigonocephaly, TRIGONOCEPHALY 2	rs281875280, rs184394424, rs200650442, rs762799389, rs556974765	21931569, 21931569, 11332973