CACNA2D4 (calcium voltage-gated channel auxiliary subunit alpha2delta 4)

Gene

• Entrez ID: 93589
• Gene name: Calcium voltage-gated channel auxiliary subunit alpha2delta 4
• Gene symbol: CACNA2D4
• Synonyms: RCD4
• Chromosome: 12
• Chromosome location: 12p13.33
• Summary: This gene encodes a member of the alpha-2/delta subunit family, a protein in the voltage-dependent calcium channel complex. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization and consist of a complex of alpha-1, a

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs71454844	G>A,T	Likely-pathogenic, uncertain-significance	Synonymous variant, stop gained, coding sequence variant
rs76064926	C>T	Benign, likely-pathogenic, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs77175207	C>G,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, missense variant
rs199888783	G>A,C	Conflicting-interpretations-of-pathogenicity	Missense variant, synonymous variant, coding sequence variant
rs200098356	G>A,C	Uncertain-significance, likely-pathogenic	Missense variant, stop gained, coding sequence variant
rs201783863	C>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs1210621191	GCCCAGC>-	Likely-pathogenic	Frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT017574	hsa-miR-335-5p	Microarray	18185580
MIRT449485	hsa-miR-7158-3p	PAR-CLIP	22100165
MIRT449484	hsa-miR-203b-3p	PAR-CLIP	22100165
MIRT449485	hsa-miR-7158-3p	PAR-CLIP	22100165
MIRT449484	hsa-miR-203b-3p	PAR-CLIP	22100165
MIRT857832	hsa-miR-1179	CLIP-seq
MIRT857833	hsa-miR-320e	CLIP-seq
MIRT857834	hsa-miR-3945	CLIP-seq
MIRT857835	hsa-miR-4252	CLIP-seq
MIRT857836	hsa-miR-4259	CLIP-seq
MIRT857837	hsa-miR-4260	CLIP-seq
MIRT857838	hsa-miR-4715-5p	CLIP-seq
MIRT857839	hsa-miR-4727-5p	CLIP-seq
MIRT857840	hsa-miR-4769-3p	CLIP-seq
MIRT857841	hsa-miR-4778-5p	CLIP-seq
MIRT857842	hsa-miR-486-3p	CLIP-seq
MIRT1954742	hsa-miR-1294	CLIP-seq
MIRT1954743	hsa-miR-4316	CLIP-seq
MIRT1954744	hsa-miR-4675	CLIP-seq
MIRT1954745	hsa-miR-4687-3p	CLIP-seq
MIRT1954746	hsa-miR-4741	CLIP-seq
MIRT1954747	hsa-miR-5096	CLIP-seq
MIRT2192313	hsa-miR-15a	CLIP-seq
MIRT2192314	hsa-miR-15b	CLIP-seq
MIRT2192315	hsa-miR-16	CLIP-seq
MIRT2192316	hsa-miR-195	CLIP-seq
MIRT2192317	hsa-miR-3144-5p	CLIP-seq
MIRT2192318	hsa-miR-3191	CLIP-seq
MIRT2192319	hsa-miR-3913-3p	CLIP-seq
MIRT857834	hsa-miR-3945	CLIP-seq
MIRT2192320	hsa-miR-424	CLIP-seq
MIRT857836	hsa-miR-4259	CLIP-seq
MIRT857837	hsa-miR-4260	CLIP-seq
MIRT2192321	hsa-miR-4524	CLIP-seq
MIRT2192322	hsa-miR-4652-5p	CLIP-seq
MIRT857838	hsa-miR-4715-5p	CLIP-seq
MIRT2192323	hsa-miR-4747-5p	CLIP-seq
MIRT857842	hsa-miR-486-3p	CLIP-seq
MIRT2192324	hsa-miR-497	CLIP-seq
MIRT2192325	hsa-miR-499-3p	CLIP-seq
MIRT2192326	hsa-miR-499a-3p	CLIP-seq
MIRT2192327	hsa-miR-503	CLIP-seq
MIRT2192328	hsa-miR-646	CLIP-seq
MIRT857834	hsa-miR-3945	CLIP-seq
MIRT857836	hsa-miR-4259	CLIP-seq
MIRT857837	hsa-miR-4260	CLIP-seq
MIRT857838	hsa-miR-4715-5p	CLIP-seq
MIRT857842	hsa-miR-486-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005245	Function	Voltage-gated calcium channel activity	IBA	21873635
GO:0005245	Function	Voltage-gated calcium channel activity	IDA	12181424
GO:0005886	Component	Plasma membrane	TAS
GO:0005891	Component	Voltage-gated calcium channel complex	IBA	21873635
GO:0005891	Component	Voltage-gated calcium channel complex	IDA	12181424
GO:0034765	Process	Regulation of ion transmembrane transport	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0050908	Process	Detection of light stimulus involved in visual perception	IMP	17033974
GO:0061337	Process	Cardiac conduction	TAS
GO:0070588	Process	Calcium ion transmembrane transport	IDA	12181424

Other IDs

• MIM: 608171
• HGNC: 20202
• e!Ensembl: ENSG00000151062

Protein

• UniProt ID: Q7Z3S7
• Protein name: Voltage-dependent calcium channel subunit alpha-2/delta-4 (Voltage-gated calcium channel subunit alpha-2/delta-4) [Cleaved into: Voltage-dependent calcium channel subunit alpha-2-4; Voltage-dependent calcium channel subunit delta-4]
• Protein function: The alpha-2/delta subunit of voltage-dependent calcium channels regulates calcium current density and activation/inactivation kinetics of the calcium channel.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF08399	VWA_N	148 → 264	VWA N-terminal	Family
  PF13768	VWA_3	290 → 455	von Willebrand factor type A domain	Domain
  PF08473	VGCC_alpha2	681 → 1110	Neuronal voltage-dependent calcium channel alpha 2acd	Family

• Sequence:

  MVCGCSALLPLPNPRPTMPATPNFLANPSSSSRWIPLQPMPVAWAFVQKTSALLWLLLLG
  TSLSPAWGQAKIPLETVKLWADTFGGDLYNTVTKYSGSLLLQKKYKDVESSLKIEEVDGL
  ELVRKFSEDMENMLRRKVEAVQNLVEAAEEADLNHEFNESLVFDYYNSVLINERDEKGNF
  VELGAEFLLESNAHFSNLPVNTSISSVQLPTNVYNKDPDILNGVYMSEALNAVFVENFQR
  DPTLTWQYFGSATGFFRIYPGIKWTPDENGVITFDCRNRGWYIQAATSPKDIVILVDVSG
  SMKGLRMTIAKHTITTILDTLGENDFINIIAYNDYVHYIEPCFKGILVQADRDNREHFKL
  LVEELMVKGVGVVDQALREAFQILKQFQEAKQGSLCNQAIMLISDGAVEDYEPVFEKYNW
  PDCKVRVFTYLIGREVSFADRMKWIACNNKGYYTQISTLADTQENVMEYLHVLSRPMVIN
  HDHDIIWTEAYMDSKLLSSQAQSLTLLTTVAMPVFSKKNETRSHGILLGVVGSDVALREL
  MKLAPRYKLGVHGYAFLNTNNGYILSHPDLRPLYREGKKLKPKPNYNSVDLSEVEWEDQA
  ESLRTAMINRETGTLSMDVKVPMDKGKRVLFLTNDYFFTDISDTPFSLGVVLSRGHGEYI
  LLGNTSVEEGLHDLLHPDLALAGDWIYCITDIDPDHRKLSQLEAMIRFLTRKDPDLECDE
  ELVREVLFDAVVTAPMEAYWTALALNMSEESEHVVDMAFLGTRAGLLRSSLFVGSEKVSD
  RKFLTPEDEASVFTLDRFPLWYRQASEHPAGSFVFNLRWAEGPESAGEPMVVTASTAVAV
  TVDKRTAIAAAAGVQMKLEFLQRKFWAATRQCSTVDGPCTQSCEDSDLDCFVIDNNGFIL
  ISKRSRETGRFLGEVDGAVLTQLLSMGVFSQVTMYDYQAMCKPSSHHHSAAQPLVSPISA
  FLTATRWLLQELVLFLLEWSVWGSWYDRGAEAKSVFHHSHKHKKQDPLQPCDTEYPVFVY
  QPAIREANGIVECGPCQKVFVVQQIPNSNLLLLVTDPTCDCSIFPPVLQEATEVKYNASV
  KCDRMRSQKLRRRPDSCHAFHPEENAQDCGGASDTSASPPLLLLPVCAWGLLPQLLR

• Sequence length: 1137

Pathways

KEGG:

MAPK signaling pathway
Cardiac muscle contraction
Adrenergic signaling in cardiomyocytes
Oxytocin signaling pathway
Hypertrophic cardiomyopathy
Arrhythmogenic right ventricular cardiomyopathy
Dilated cardiomyopathy

Reactome:

Phase 0 - rapid depolarisation
Phase 2 - plateau phase

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Cone-rod dystrophy	Cone-Rod Dystrophy 2, Cone rod dystrophy, Cone-Rod Dystrophies	rs200691042, rs121908281, rs28940314, rs121434337, rs80338903, rs121909398, rs28937883, rs397515360, rs137853006, rs786205085, rs137853040, rs137853041, rs786205086, rs104894671, rs1568626209, rs104894672, rs61748436, rs2123743692, rs61751408, rs61751374, rs61750200, rs62642560, rs61752410, rs121909206, rs387906388, rs61753033, rs61750172, rs61750173, rs267606857, rs606231180, rs606231181, rs137852551, rs863223294, rs61755792, rs61755786, rs62625014, rs781781440, rs137853932, rs1064792853, rs387907136, rs397517974, rs397517994, rs786200944, rs398123044, rs398122960, rs61752435, rs1800728, rs398124354, rs61749679, rs61750184, rs61755781, rs281865373, rs62653029, rs62635009, rs281865297, rs61748558, rs61749409, rs61750202, rs61750065, rs61751398, rs61750146, rs281865377, rs61751388, rs62646861, rs61750158, rs61751403, rs62646872, rs61750575, rs61751407, rs61750645, rs281865516, rs61751266, rs137853907, rs483353055, rs587777469, rs587777470, rs587777471, rs199882533, rs76216585, rs587777693, rs587777694, rs786205151, rs150115958, rs2723341, rs201422368, rs786205664, rs746559651, rs786205665, rs786205661, rs794727197, rs192003551, rs886041039, rs863224913, rs771214648, rs863225090, rs751163782, rs875989778, rs886044750, rs768278935, rs886044735, rs201471607, rs61752398, rs878853400, rs886037880, rs886037881, rs886039559, rs748706582, rs886039882, rs886041900, rs886042153, rs749526785, rs1057516195, rs1057516199, rs543698823, rs199840367, rs752175052, rs1085307121, rs104893793, rs1064797182, rs1131691378, rs778234759, rs1553193813, rs373331232, rs756678484, rs780667159, rs1557110499, rs1553901823, rs201587670, rs1439202144, rs1555635778, rs1429786931, rs1553187160, rs1553188916, rs1555345387, rs61749412, rs951379922, rs1554186472, rs767528365, rs1210104601, rs776289402, rs750740765, rs544616523, rs75459701, rs759940113, rs1557787559, rs782581701, rs771116776, rs1006935198, rs755733328, rs1560141393, rs121918567, rs752263228, rs775957498, rs1030149008, rs530749007, rs141823837, rs1570393848, rs1571250020, rs1570382663, rs78484040, rs766357803, rs1437021651, rs1601982595, rs1597331616, rs748798324, rs759408031, rs747512450, rs373680665, rs1355802816, rs374017889, rs1589307705, rs376500610, rs1598146173, rs1598149154, rs752619497, rs1571257937, rs1572829866, rs1426009756, rs1464167194, rs1588391640, rs1588865728, rs1589306127, rs1420750126, rs1598150539, rs1598150793, rs1601972449, rs782740998, rs767366723, rs1602653110, rs778456901, rs1662213462, rs1662507319, rs751644763, rs1689012192, rs1667508280, rs1719285721, rs1734066547, rs1800111659, rs1827340429, rs1196886096, rs1882924778, rs2046020472, rs2046113301, rs1594280740, rs1590681805, rs1570373408, rs369973540, rs1005271380, rs368213921, rs535922252, rs745741473, rs138370992, rs772656461, rs749738655, rs1968173024, rs746128841, rs1887576038, rs909373397, rs750116711, rs1659840790, rs1768016995, rs1186795749	17033974
Congenital stationary night blindness	Congenital stationary night blindness	rs786205249, rs80338903, rs62638214, rs62638624, rs62638202, rs62638197, rs766862238, rs267607140, rs267607141, rs62638191, rs62638193, rs62637021, rs62637027, rs104894910, rs104894911, rs122456133, rs122456134, rs122456135, rs2147483647, rs104893789, rs104893790, rs104893796, rs121918582, rs104893740, rs80359870, rs387906862, rs786205113, rs772011426, rs281875234, rs794726685, rs387907138, rs773126191, rs770066665, rs794726686, rs397509379, rs397509380, rs61750168, rs281865186, rs281865194, rs150115958, rs786205852, rs786205853, rs786205854, rs778390089, rs869312176, rs879253773, rs879253774, rs886039559, rs886039560, rs886043488, rs1057518829, rs104893793, rs1553186509, rs61751398, rs781463257, rs531851447, rs770380556, rs748046539, rs1555418784, rs1555424166, rs781610444, rs1555424849, rs1555966753, rs1555967281, rs1557106008, rs1557107192, rs1557107417, rs1557108147, rs1557109796, rs1557109912, rs1557110046, rs1557110192, rs1557110499, rs1557110988, rs372529012, rs374913800, rs1410075831, rs766780281, rs1555967031, rs1566945534, rs777989874, rs782581701, rs1485132228, rs1567728372, rs1567725425, rs150441866, rs1358925739, rs779821510, rs1590998813, rs1594580431, rs777168556, rs763546583, rs1290420698, rs765645888, rs1596029830, rs1602180478, rs1602180791, rs1602181006, rs1602181043, rs1602181253, rs1602627593, rs782740998, rs1602630650, rs1602639607, rs1602641426, rs1602644716, rs1602658505, rs1602628429, rs2065841382, rs1596017653, rs769355168, rs1578278438, rs984572250, rs775166854, rs2065717735
Myopia	Severe myopia	rs387907109, rs146936371, rs587776903, rs786205127, rs398122836, rs199624584, rs587777625, rs786205216, rs758872875, rs764211125, rs1135402746, rs765658563, rs1555941129, rs1555941116, rs199923805, rs782555528, rs1554862601, rs1586620121, rs1387950081, rs2051026773, rs1422332023
Nystagmus	Nystagmus	rs137852207, rs137852208, rs1928435502, rs137852209, rs137852210, rs1929191668, rs137852211, rs137852212, rs2124209414, rs387906720, rs387906721, rs1602791884, rs786205896
Retinal cone dystrophy	RETINAL CONE DYSTROPHY 4	rs200311463	26560832

Unknown
Disease name	Disease term	dbSNP ID	References
Disorder of eye	Disorder of eye
Hypoplasia of optic disc	Hypoplasia of optic disc
Night blindness	Night blindness, congenital stationary		26560832, 19578023
Nyctalopia	Nyctalopia
Strabismus	Strabismus