FRMD7 (FERM domain containing 7)

Gene

• Entrez ID: 90167
• Gene name: FERM domain containing 7
• Gene symbol: FRMD7
• Synonyms (NCBI Gene): NYS, NYS1, XIPAN
• Chromosome: X
• Chromosome location: Xq26.2
• Summary: Mutations in this gene are associated with X-linked congenital nystagmus. [provided by RefSeq, Dec 2008]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs137852207	G>A	Pathogenic	Coding sequence variant, stop gained
rs137852208	G>A	Pathogenic	Coding sequence variant, stop gained
rs137852209	C>T	Pathogenic	Missense variant, synonymous variant, coding sequence variant, intron variant, genic upstream transcript variant
rs137852210	C>T	Pathogenic	Coding sequence variant, intron variant, missense variant, genic upstream transcript variant
rs137852211	A>C	Pathogenic	Coding sequence variant, 5 prime UTR variant, missense variant
rs137852212	G>A,C	Pathogenic	Coding sequence variant, missense variant
rs387906720	A>C,T	Pathogenic	Missense variant, coding sequence variant
rs387906721	C>A,T	Pathogenic	Missense variant, coding sequence variant
rs786205896	T>C	Pathogenic	Missense variant, coding sequence variant
rs886041507	C>T	Pathogenic	Splice donor variant
rs1602791884	C>T	Pathogenic	Intron variant
rs1602818287	C>G	Likely-pathogenic	Coding sequence variant, genic upstream transcript variant, missense variant, intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT024029	hsa-miR-1-3p	Microarray	18668037
MIRT1004746	hsa-miR-34b	CLIP-seq
MIRT1004747	hsa-miR-34c-3p	CLIP-seq
MIRT1004748	hsa-miR-3661	CLIP-seq
MIRT1004749	hsa-miR-3685	CLIP-seq
MIRT1004750	hsa-miR-384	CLIP-seq
MIRT1004751	hsa-miR-433	CLIP-seq
MIRT1004752	hsa-miR-4464	CLIP-seq
MIRT1004753	hsa-miR-4704-3p	CLIP-seq
MIRT1004754	hsa-miR-4748	CLIP-seq
MIRT1004755	hsa-miR-4760-3p	CLIP-seq
MIRT1004756	hsa-miR-495	CLIP-seq
MIRT1004757	hsa-miR-577	CLIP-seq
MIRT1004758	hsa-miR-631	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005085	Function	Guanyl-nucleotide exchange factor activity	IBA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005615	Component	Extracellular space	HDA	22664934
GO:0005654	Component	Nucleoplasm	IDA
GO:0005829	Component	Cytosol	IDA
GO:0005886	Component	Plasma membrane	IDA
GO:0007399	Process	Nervous system development	IEA
GO:0010592	Process	Positive regulation of lamellipodium assembly	IEA
GO:0010975	Process	Regulation of neuron projection development	IBA
GO:0010975	Process	Regulation of neuron projection development	IEA
GO:0010975	Process	Regulation of neuron projection development	ISS
GO:0030426	Component	Growth cone	IEA
GO:0030426	Component	Growth cone	ISS
GO:0042995	Component	Cell projection	IEA
GO:0043005	Component	Neuron projection	IEA
GO:0043005	Component	Neuron projection	ISS
GO:0043025	Component	Neuronal cell body	IEA
GO:0043025	Component	Neuronal cell body	ISS
GO:0051057	Process	Positive regulation of small GTPase mediated signal transduction	IEA
GO:0051497	Process	Negative regulation of stress fiber assembly	IEA

Other IDs

• MIM: 300628
• HGNC: 8079
• e!Ensembl: ENSG00000165694

Protein

• UniProt ID: Q6ZUT3
• Protein name: FERM domain-containing protein 7
• Protein function: Plays a role in neurite development, may be through the activation of the GTPase RAC1. Plays a role in the control of eye movement and gaze stability.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF09379	FERM_N	6 → 69	FERM N-terminal domain	Domain
  PF00373	FERM_M	85 → 192	FERM central domain	Domain
  PF09380	FERM_C	196 → 286	FERM C-terminal PH-like domain	Domain
  PF08736	FA	291 → 334	FERM adjacent (FA)	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed in liver, kidney, pancreas and at low levels in brain and heart. Expressed in embryonic brain and developing neural retina. {ECO:0000269|PubMed:17013395}.
• Sequence:

  MLHLKVQFLDDSQKIFVVDQKSSGKALFNLSCSHLNLAEKEYFGLEFCSHSGNNVWLELL
  KPITKQVKNPKEIVFKFMVKFFPVDPGHLREELTRYLFTLQIKKDLALGRLPCSDNCTAL
  MVSHILQSELGDFHEETDRKHLAQTRYLPNQDCLEGKIMHFHQKHIGRSPAESDILLLDI
  ARKLDMYGIRPHPASDGEGMQIHLAVAHMGVLVLRGNTKINTFNWAKIRKLSFKRKHFLI
  KLHANILVLCKDTLEFTMASRDACKAFWKTCVEYHAFFRLSEEPKSKPKTLLCSKGSSFR
  YSGRTQRQLLEYGRKGRLKSLPFERKHYPSQYHERQCRSSPDLLSDVSKQVEDLRLAYGG
  GYYQNVNGVHASEPVLESRRRNSALEVTFATELEHSKPEADPTLLHQSQSSSSFPFIYMD
  PVFNTEPNPNPDPRDIFSERSSLSSFQTSCKFSGNHMSIYSGLTSKVRPAKQLTYTDVPY
  IPCTGQQVGIMPPQVFFYVDKPPQVPRWSPIRAEERTSPHSYVEPTAMKPAERSPRNIRM
  KSFQQDLQVLQEAIARTSGRSNINVGLEEEDPNLEDAFVCNIQEQTPKRSQSQSDMKTIR
  FPFGSEFRPLGPCPALSHKADLFTDMFAEQELPAVLMDQSTAERYVASESSDSESEILKP
  DYYALYGKEIRSPMARIRLSSGSLQLDEEDEDAYFNTPTAEDRTSLKPCNYFLA

• Sequence length: 714

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Nystagmus 1, congenital, X-linked	Likely pathogenic; Pathogenic	rs1429474154, rs1332489637, rs2520731322, rs786205896, rs1297486092, rs137852207, rs137852208, rs1928435502, rs137852209, rs137852210, rs1929191668, rs137852211, rs137852212, rs2124209414, rs387906720, rs387906721, rs1602791884, rs1927753913, rs1927850772	RCV005253800 RCV005867172 RCV002291128 RCV000172871 RCV004587468 RCV000011529 RCV000011530 RCV000011531 RCV000011532 RCV000011533 RCV000011534 RCV000011535 RCV000011536 RCV000011537 RCV000022868 RCV000022869 RCV000022870 RCV001253283 RCV003225169	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Retinal dystrophy	Pathogenic	rs1928365871	RCV001074068	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Thyroid cancer, nonmedullary, 1	Likely pathogenic	rs1297486092	RCV005927043	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
FRMD7-related disorder	Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Infantile Nystagmus	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NYSTAGMUS 1, CONGENITAL, X- LINKED	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Achromatopsia	Achromatopsia	BEFREE	21951007		★☆☆☆☆ Found in Text Mining only
Albinism	Albinism	BEFREE	21220551, 24346039		★☆☆☆☆ Found in Text Mining only
Albinism	Albinism	Pubtator	35157951, 35488210	Associate	★☆☆☆☆ Found in Text Mining only
Albinism, Ocular	Ocular albinism	BEFREE	30942644		★☆☆☆☆ Found in Text Mining only
Congenital cataract	Congenital Cataract	BEFREE	30890130		★☆☆☆☆ Found in Text Mining only
Congenital Fibrosis of the Extraocular Muscles	Congenital fibrosis of extraocular muscles	BEFREE	21746984		★☆☆☆☆ Found in Text Mining only
Congenital Mesoblastic Nephroma	Congenital Mesoblastic Nephroma	BEFREE	17893669		★☆☆☆☆ Found in Text Mining only
Congenital nystagmus	Congenital nystagmus	BEFREE	17013395, 18246032, 19072571, 22065930, 22262942, 22490987, 23733424, 23946638, 24169426, 24434814, 25916882, 28764992, 30015830, 30576400, 30890130, 30942644		★☆☆☆☆ Found in Text Mining only
Congenital nystagmus	Congenital nystagmus	LHGDN	17397053, 18247295, 19072571		★☆☆☆☆ Found in Text Mining only
Congenital nystagmus	Congenital nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cystic Fibrosis	Cystic Fibrosis	BEFREE	26293390		★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	24688117	Associate	★☆☆☆☆ Found in Text Mining only
Horizontal Nystagmus	Horizontal nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	Pubtator	37749571, 38243264	Associate	★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	19892780, 28962155		★☆☆☆☆ Found in Text Mining only
NON RARE IN EUROPE: Idiopathic infantile nystagmus	Nystagmus	Orphanet			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	BEFREE	17768376, 17846367, 17962394, 18161616, 18372314, 18431453, 19892780, 20450309, 21220551, 22065930, 22490987, 23406872, 24688117, 26160353, 26268155, 30025138, 30576400, 30618027		★☆☆☆☆ Found in Text Mining only
Nystagmus 1 congenital X linked	Nystagmus	Pubtator	22065930	Associate	★☆☆☆☆ Found in Text Mining only
Nystagmus 1, congenital, X- linked	Nystagmus	GENOMICS_ENGLAND_DG	17013395, 17846367, 18087240, 18431453		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nystagmus 1, congenital, X- linked	Nystagmus	UNIPROT_DG	17013395, 17397053, 17768376, 17893669, 17962394, 18087240, 18246032, 18431453, 21303855, 21365021, 22490987, 23946638		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nystagmus 1, congenital, X- linked	Nystagmus	CTD_human_DG	19892780		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nystagmus 1, congenital, X- linked	Nystagmus	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nystagmus Congenital	Nystagmus	Pubtator	10090899, 22262942, 22490987, 24169426, 38279119	Associate	★☆☆☆☆ Found in Text Mining only
Nystagmus Pathologic	Nystagmus	Pubtator	21303855, 22490987, 23406872, 24688117, 26268155, 27036142, 30576400, 31743612, 38279119	Associate	★☆☆☆☆ Found in Text Mining only
Pendular Nystagmus	Pendular nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Periodic Alternating Nystagmus	Nystagmus	BEFREE	21303855		★☆☆☆☆ Found in Text Mining only
Progressive hearing loss stapes fixation	Hearing loss with stapes fixation	Pubtator	37749571	Associate	★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	BEFREE	18372314		★☆☆☆☆ Found in Text Mining only