SPTBN4 (spectrin beta, non-erythrocytic 4)

Gene

• Entrez ID: 57731
• Gene name: Spectrin beta, non-erythrocytic 4
• Gene symbol: SPTBN4
• Synonyms: CMND, NEDHND, QV, SPNB4, SPTBN3
• Chromosome: 19
• Chromosome location: 19q13.2
• Summary: Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is compo

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs765087147	G>A	Pathogenic	Genic upstream transcript variant, missense variant, coding sequence variant
rs777273785	C>A,T	Pathogenic	Missense variant, intron variant, coding sequence variant, genic downstream transcript variant
rs864309618	G>A	Uncertain-significance, pathogenic	Genic upstream transcript variant, coding sequence variant, stop gained
rs1114167445	C>T	Pathogenic	Coding sequence variant, stop gained, genic upstream transcript variant
rs1555721549	G>-	Pathogenic	Frameshift variant, coding sequence variant, downstream transcript variant, genic downstream transcript variant
rs1555815437	->AGCGGGCGGCGCGCATGACC	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, frameshift variant
rs1555818396	G>T	Pathogenic	Genic upstream transcript variant, coding sequence variant, stop gained
rs1599759068	GC>-	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, frameshift variant
rs1599794560	G>T	Likely-pathogenic	Splice donor variant, genic downstream transcript variant
rs1599819198	->ATGAGGCC	Likely-pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1386928	hsa-let-7a	CLIP-seq
MIRT1386929	hsa-let-7b	CLIP-seq
MIRT1386930	hsa-let-7c	CLIP-seq
MIRT1386931	hsa-let-7d	CLIP-seq
MIRT1386932	hsa-let-7e	CLIP-seq
MIRT1386933	hsa-let-7f	CLIP-seq
MIRT1386934	hsa-let-7g	CLIP-seq
MIRT1386935	hsa-let-7i	CLIP-seq
MIRT1386936	hsa-miR-103a	CLIP-seq
MIRT1386937	hsa-miR-107	CLIP-seq
MIRT1386938	hsa-miR-1293	CLIP-seq
MIRT1386939	hsa-miR-1294	CLIP-seq
MIRT1386940	hsa-miR-1324	CLIP-seq
MIRT1386941	hsa-miR-202	CLIP-seq
MIRT1386942	hsa-miR-3179	CLIP-seq
MIRT1386943	hsa-miR-3202	CLIP-seq
MIRT1386944	hsa-miR-3714	CLIP-seq
MIRT1386945	hsa-miR-3922-5p	CLIP-seq
MIRT1386946	hsa-miR-4310	CLIP-seq
MIRT1386947	hsa-miR-4447	CLIP-seq
MIRT1386948	hsa-miR-4458	CLIP-seq
MIRT1386949	hsa-miR-4472	CLIP-seq
MIRT1386950	hsa-miR-4481	CLIP-seq
MIRT1386951	hsa-miR-4483	CLIP-seq
MIRT1386952	hsa-miR-4484	CLIP-seq
MIRT1386953	hsa-miR-4500	CLIP-seq
MIRT1386954	hsa-miR-4651	CLIP-seq
MIRT1386955	hsa-miR-4710	CLIP-seq
MIRT1386956	hsa-miR-4745-5p	CLIP-seq
MIRT1386957	hsa-miR-4747-5p	CLIP-seq
MIRT1386958	hsa-miR-4756-3p	CLIP-seq
MIRT1386959	hsa-miR-4758-5p	CLIP-seq
MIRT1386960	hsa-miR-4792	CLIP-seq
MIRT1386961	hsa-miR-548an	CLIP-seq
MIRT1386962	hsa-miR-608	CLIP-seq
MIRT1386963	hsa-miR-98	CLIP-seq
MIRT2115814	hsa-miR-1180	CLIP-seq
MIRT2115815	hsa-miR-1226	CLIP-seq
MIRT1386938	hsa-miR-1293	CLIP-seq
MIRT1386951	hsa-miR-4483	CLIP-seq
MIRT1386954	hsa-miR-4651	CLIP-seq
MIRT2115816	hsa-miR-4664-3p	CLIP-seq
MIRT2115817	hsa-miR-4667-3p	CLIP-seq
MIRT1386955	hsa-miR-4710	CLIP-seq
MIRT2115818	hsa-miR-4733-3p	CLIP-seq
MIRT1386960	hsa-miR-4792	CLIP-seq
MIRT1386962	hsa-miR-608	CLIP-seq
MIRT2460492	hsa-miR-1321	CLIP-seq
MIRT2460493	hsa-miR-1915	CLIP-seq
MIRT2460494	hsa-miR-2355-5p	CLIP-seq
MIRT2460495	hsa-miR-4270	CLIP-seq
MIRT2460496	hsa-miR-4441	CLIP-seq
MIRT2460497	hsa-miR-4739	CLIP-seq
MIRT2460498	hsa-miR-4756-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000165	Process	MAPK cascade	TAS
GO:0002028	Process	Regulation of sodium ion transport	ISS
GO:0003779	Function	Actin binding	ISS
GO:0005200	Function	Structural constituent of cytoskeleton	TAS	11294830
GO:0005515	Function	Protein binding	IPI	11086001, 12812986
GO:0005543	Function	Phospholipid binding	IEA
GO:0005737	Component	Cytoplasm	IDA	11294830
GO:0005829	Component	Cytosol	TAS
GO:0005884	Component	Actin filament	ISS
GO:0005886	Component	Plasma membrane	ISS
GO:0005912	Component	Adherens junction	ISS
GO:0006888	Process	Endoplasmic reticulum to Golgi vesicle-mediated transport	TAS
GO:0007010	Process	Cytoskeleton organization	IEA
GO:0007409	Process	Axonogenesis	ISS
GO:0007411	Process	Axon guidance	TAS
GO:0007605	Process	Sensory perception of sound	ISS
GO:0007628	Process	Adult walking behavior	ISS
GO:0008091	Component	Spectrin	IDA	11086001
GO:0009566	Process	Fertilization	IEA
GO:0010459	Process	Negative regulation of heart rate	ISS
GO:0014704	Component	Intercalated disc	IEA
GO:0016020	Component	Membrane	IDA	11086001
GO:0016192	Process	Vesicle-mediated transport	TAS	11294830
GO:0016363	Component	Nuclear matrix	IDA	11294830
GO:0016605	Component	PML body	IDA	11294830
GO:0019226	Process	Transmission of nerve impulse	ISS
GO:0019902	Function	Phosphatase binding	IPI	11086001
GO:0021952	Process	Central nervous system projection neuron axonogenesis	ISS
GO:0030506	Function	Ankyrin binding	IDA	11294830
GO:0030507	Function	Spectrin binding	ISS
GO:0033135	Process	Regulation of peptidyl-serine phosphorylation	ISS
GO:0033268	Component	Node of Ranvier	ISS
GO:0033270	Component	Paranode region of axon	IEA
GO:0040018	Process	Positive regulation of multicellular organism growth	IEA
GO:0043025	Component	Neuronal cell body	ISS
GO:0043194	Component	Axon initial segment	ISS
GO:0043203	Component	Axon hillock	ISS
GO:0045162	Process	Clustering of voltage-gated sodium channels	ISS
GO:0051693	Process	Actin filament capping	IEA
GO:0061337	Process	Cardiac conduction	ISS
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:0070852	Component	Cell body fiber	ISS
GO:0072659	Process	Protein localization to plasma membrane	ISS
GO:0106006	Function	Cytoskeletal protein-membrane anchor activity	TAS	11086001

Other IDs

• MIM: 606214
• HGNC: 14896
• e!Ensembl: ENSG00000160460

Protein

• UniProt ID: Q9H254
• Protein name: Spectrin beta chain, non-erythrocytic 4 (Beta-IV spectrin) (Spectrin, non-erythroid beta chain 3)
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00307	CH	61 → 166	Calponin homology (CH) domain	Domain
  PF00307	CH	180 → 286	Calponin homology (CH) domain	Domain
  PF00435	Spectrin	309 → 419	Spectrin repeat	Domain
  PF00435	Spectrin	429 → 533	Spectrin repeat	Domain
  PF00435	Spectrin	535 → 642	Spectrin repeat	Domain
  PF00435	Spectrin	773 → 879	Spectrin repeat	Domain
  PF00435	Spectrin	881 → 985	Spectrin repeat	Domain
  PF00435	Spectrin	1088 → 1197	Spectrin repeat	Domain
  PF00435	Spectrin	1305 → 1408	Spectrin repeat	Domain
  PF00435	Spectrin	1410 → 1513	Spectrin repeat	Domain
  PF00435	Spectrin	1515 → 1619	Spectrin repeat	Domain
  PF00435	Spectrin	1622 → 1725	Spectrin repeat	Domain
  PF00435	Spectrin	1727 → 1832	Spectrin repeat	Domain
  PF00435	Spectrin	1834 → 1939	Spectrin repeat	Domain
  PF00435	Spectrin	1942 → 2046	Spectrin repeat	Domain
  PF00435	Spectrin	2048 → 2127	Spectrin repeat	Domain
  PF15410	PH_9	2420 → 2527	Pleckstrin homology domain	Domain

• Sequence:

  MAQVPGEVDNMEGLPAPNNNPAARWESPDRGWEREQPAASTAAASLFECSRIKALADERE
  AVQKKTFTKWVNSHLARVGCHIGDLYVDLRDGFVLTRLLEVLSGEQLPRPTRGRMRIHSL
  ENVDKALQFLKEQRVHLENVGSHDIVDGNHRLTLGLVWTIILRFQIQVIKIETEDNRETR
  SAKDALLLWCQMKTAGYPEVNIQNFTTSWRDGLAFNALIHRHRPDLVDFSKLTKSNANYN
  LQRAFRTAEQHLGLARLLDPEDVNMEAPDEKSIITYVVSFYHYFSKMKALAVEGKRIGKV
  LDQVLEVGKIIERYEELAAELLAWIHRTVGLISNQKFANSLSGVQQQLQAFTAYCTLEKP
  VKFQEKGNLEVLLFSIQSKLRACNRRLFVPREGCGIWDIDKAWGELEKAEHEREAALRAE
  LIRQEKLELLAQRFDHKVAMRESWLNENQRLVSQDNFGYELPAVEAAMKKHEAIEADIAA
  YEERVQGVAELAQALAAEGYYDIRRVAAQRDSVLRQWALLTGLVGARRTRLEQNLALQKV
  FQEMVYMVDWMEEMQAQLLSRECGQHLVEADDLLQKHGLLEGDIAAQSERVEALNAAALR
  FSQLQGYQPCDPQVICNRVNHVHGCLAELQEQAARRRAELEASRSLWALLQELEEAESWA
  RDKERLLEAAGGGGAAGAAGAAGTAGGAHDLSSTARLLAQHKILQGELGGRRALLQQALR
  CGEELVAAGGAVGPGADTVHLVGLAERAASARRRWQRLEEAAARRERRLQEARALHQFGA
  DLDGLLDWLRDAYRLAAAGDFGHDEASSRRLARQHRALTGEVEAHRGPVSGLRRQLATLG
  GASGAGPLVVALQVRVVEAEQLFAEVTEVAALRRQWLRDALAVYRMFGEVHACELWIGEK
  EQWLLSMRVPDSLDDVEVVQHRFESLDQEMNSLMGRVLDVNHTVQELVEGGHPSSDEVRS
  CQDHLNSRWNRIVELVEQRKEEMSAVLLVENHVLEVAEVRAQVREKRRAVESAPRAGGAL
  QWRLSGLEAALQALEPRQAALLEEAALLAERFPAQAARLHQGAEELGAEWGALASAAQAC
  GEAVAAAGRLQRFLHDLDAFLDWLVRAQEAAGGSEGPLPNSLEEADALLARHAALKEEVD
  QREEDYARIVAASEALLAADGAELGPGLALDEWLPHLELGWHKLLGLWEARREALVQAHI
  YQLFLRDLRQALVVLRNQEMALSGAELPGTVESVEEALKQHRDFLTTMELSQQKMQVAVQ
  AAEGLLRQGNIYGEQAQEAVTRLLEKNQENQLRAQQWMQKLHDQLELQHFLRDCHELDGW
  IHEKMLMARDGTREDNHKLHKRWLRHQAFMAELAQNKEWLEKIEREGQQLMQEKPELAAS
  VRKKLGEIRQCWAELESTTQAKARQLFEASKADQLVQSFAELDKKLLHMESQLQDVDPGG
  DLATVNSQLKKLQSMESQVEEWYREVGELQAQTAALPLEPASKELVGERQNAVGERLVRL
  LEPLQERRRLLLASKELHQVAHDLDDELAWVQERLPLAMQTERGNGLQAVQQHIKKNQGL
  RREIQAHGPRLEEVLERAGALASLRSPEAEAVRRGLEQLQSAWAGLREAAERRQQVLDAA
  FQVEQYYFDVAEVEAWLGEQELLMMSEDKGKDEQSTLQLLKKHLQLEQGVENYEESIAQL
  SRQCRALLEMGHPDSEQISRRQSQVDRLYVALKELGEERRVALEQQYWLYQLSRQVSELE
  HWIAEKEVVAGSPELGQDFEHVSVLQEKFSEFASETGMAGRERLAAVNQMVDELIECGHT
  AAATMAEWKDGLNEAWAELLELMGTRAQLLAASRELHKFFSDARELQGQIEEKRRRLPRL
  TTPPEPRPSASSMQRTLRAFEHDLQLLVSQVRQLQEGAAQLRTVYAGEHAEAIASREQEV
  LQGWKELLSACEDARLHVSSTADALRFHSQVRDLLSWMDGIASQIGAADKPRDVSSVEVL
  MNYHQGLKTELEARVPELTTCQELGRSLLLNKSAMADEIQAQLDKLGTRKEEVSEKWDRH
  WEWLQQMLEVHQFAQEAVVADAWLTAQEPLLQSRELGSSVDEVEQLIRRHEAFRKAAAAW
  EERFSSLRRLTTIEKIKAEQSKQPPTPLLGRKFFGDPTELAAKAAPLLRPGGYERGLEPL
  ARRASDTLSAEVRTRVGYVRQELKPERLQPRIDRLPEIPGRVEPAALPAAPEDAAETPAT
  PAAAEQVRPRPERQESADRAEELPRRRRPERQESVDQSEEAARRRRPERQESAEHEAAHS
  LTLGRYEQMERRRERRERRLERQESSEQEMPIRGDLVKGKATLADIVEQLQEKEAGPGLP
  AGPSLPQPRELPPGRLPNGLELPERTPRPDRPRARDRPKPRRRPRPREGGEGGGSRRSRS
  APAQGGSAPAPPPPPTHTVQHEGFLLRKRELDANRKSSNRSWVSLYCVLSKGELGFYKDS
  KGPASGSTHGGEPLLSLHKATSEVASDYKKKKHVFKLQTQDGSEFLLQAKDEEEMNGWLE
  AVASSVAEHAEIARWGQTLPTTSSTDEGNPKREGGDRRASGRRK

• Sequence length: 2564

Pathways

KEGG:

Cytoskeleton in muscle cells

Reactome:

NCAM signaling for neurite out-growth
Interaction between L1 and Ankyrins
RAF/MAP kinase cascade
COPI-mediated anterograde transport

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291, rs886041382, rs1057518991, rs1057518699, rs753254213, rs748294403, rs762552974, rs1135401795, rs1553121073, rs1553122926, rs1364690005, rs1554086554, rs1554210415, rs1554168326, rs1554776342, rs1553873247, rs1567860112, rs779009256, rs1557447255, rs1564568350, rs780011005, rs1597464953, rs1200336864, rs1569513017, rs1587459606, rs1570332505, rs748888652, rs1575155995, rs2087029320, rs1589669105, rs1601769604, rs1184981709, rs749201074
Neurodevelopmental disorder with hypotonia, neuropathy, and deafness	NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA, NEUROPATHY, AND DEAFNESS	rs1114167445, rs1555818396, rs777273785, rs1555721549, rs1599794560	28540413
Papillary renal carcinoma	Papillary Renal Cell Carcinoma	rs5030823, rs2137087134, rs121913668, rs121913669, rs121913670, rs121913671, rs121913673, rs121913243, rs786202724	22138691
Renal carcinoma	Renal Cell Carcinoma, Conventional (Clear Cell) Renal Cell Carcinoma, Sarcomatoid Renal Cell Carcinoma, Collecting Duct Carcinoma of the Kidney	rs121913668, rs121913670, rs121913243, rs786202724	22138691
Scoliosis	Scoliosis, unspecified	rs1057518828, rs147296805, rs758163506, rs1555613564, rs1596852902, rs1596853067, rs1596853085

Unknown
Disease name	Disease term	dbSNP ID	References
Amyotrophy	Generalized amyotrophy
Central visual impairment	Central visual impairment
Chromophobe carcinoma	Chromophobe Renal Cell Carcinoma	rs137853247	22138691
Demyelinating neuropathy	Peripheral demyelinating neuropathy
Distal amyotrophy	Distal amyotrophy	rs1457770815
Facial paralysis	Facial paralysis
High palate	Byzanthine arch palate
Sclerocystic ovaries	Sclerocystic Ovaries		21411543
Polycystic ovary syndrome	Polycystic Ovary Syndrome		21411543