Incidental Mutation 'R7188:Cacna1d'
ID 559449
Institutional Source Beutler Lab
Gene Symbol Cacna1d
Ensembl Gene ENSMUSG00000015968
Gene Name calcium channel, voltage-dependent, L type, alpha 1D subunit
Synonyms Cacnl1a2, Cchl1a2, C79217, Cchl1a, Cav1.3alpha1, 8430418G19Rik, D-LTCC
MMRRC Submission 045272-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.900) question?
Stock # R7188 (G1)
Quality Score 225.009
Status Not validated
Chromosome 14
Chromosomal Location 29761898-30213113 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 29811790 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Glycine at position 1309 (S1309G)
Ref Sequence ENSEMBL: ENSMUSP00000107869 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000112249] [ENSMUST00000112250] [ENSMUST00000223803] [ENSMUST00000224198] [ENSMUST00000224395] [ENSMUST00000224785]
AlphaFold Q99246
Predicted Effect probably benign
Transcript: ENSMUST00000112249
AA Change: S1287G

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000107868
Gene: ENSMUSG00000015968
AA Change: S1287G

DomainStartEndE-ValueType
low complexity region 1 10 N/A INTRINSIC
low complexity region 54 67 N/A INTRINSIC
Pfam:Ion_trans 163 405 4.8e-59 PFAM
PDB:4DEY|B 406 502 3e-38 PDB
low complexity region 503 517 N/A INTRINSIC
Pfam:Ion_trans 557 751 5.5e-46 PFAM
low complexity region 766 781 N/A INTRINSIC
low complexity region 819 840 N/A INTRINSIC
Pfam:Ion_trans 921 1151 7.2e-51 PFAM
Pfam:Ion_trans 1239 1448 3.6e-67 PFAM
Pfam:PKD_channel 1285 1455 1.9e-9 PFAM
Blast:EFh 1469 1497 2e-9 BLAST
Ca_chan_IQ 1583 1617 5.05e-16 SMART
low complexity region 1649 1661 N/A INTRINSIC
low complexity region 1722 1728 N/A INTRINSIC
low complexity region 1830 1840 N/A INTRINSIC
low complexity region 1885 1905 N/A INTRINSIC
low complexity region 1921 1936 N/A INTRINSIC
low complexity region 2122 2133 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000112250
AA Change: S1309G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000107869
Gene: ENSMUSG00000015968
AA Change: S1309G

DomainStartEndE-ValueType
low complexity region 76 89 N/A INTRINSIC
Pfam:Ion_trans 147 439 5.6e-72 PFAM
low complexity region 473 482 N/A INTRINSIC
low complexity region 525 539 N/A INTRINSIC
Pfam:Ion_trans 544 784 2e-56 PFAM
low complexity region 788 803 N/A INTRINSIC
low complexity region 841 862 N/A INTRINSIC
Pfam:Ion_trans 907 1185 2.6e-63 PFAM
Pfam:Ion_trans 1226 1482 1.7e-70 PFAM
Pfam:PKD_channel 1306 1477 1.2e-9 PFAM
Pfam:GPHH 1484 1553 2.3e-38 PFAM
Ca_chan_IQ 1605 1639 5.05e-16 SMART
Pfam:CAC1F_C 1649 2165 1.1e-68 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000223803
AA Change: S1287G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
Predicted Effect probably benign
Transcript: ENSMUST00000224198
AA Change: S1307G

PolyPhen 2 Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
Predicted Effect probably benign
Transcript: ENSMUST00000224395
Predicted Effect probably benign
Transcript: ENSMUST00000224785
AA Change: S1287G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Predicted Effect probably benign
Transcript: ENSMUST00000224912
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a pore-forming subunit of the L-type, voltage-activated calcium channel family. These channels have been found to play a role in heart and smooth muscle contraction and in the transmission of auditory information. Homozygous knockout mice for this gene exhibit deafness and heart defects. These channels have also been linked to mitochondrial oxidative stress in a mouse model of Parkinson's disease. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2014]
PHENOTYPE: Homozygotes for targeted mutations exhibit small size, hypoinsulinemia, glucose intolerance, decreased number and size of pancreatic islets, deafness with degeneration of hair cells, bradycardia, and arrhythmia. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca17 T C 17: 24,554,600 (GRCm39) Y118C possibly damaging Het
Abcb6 A G 1: 75,150,781 (GRCm39) probably null Het
Acox2 T A 14: 8,252,996 (GRCm38) I236L possibly damaging Het
Adamts12 A T 15: 11,336,411 (GRCm39) K1499* probably null Het
Ankrd24 G T 10: 81,472,224 (GRCm39) E20* probably null Het
Arsa A T 15: 89,359,830 (GRCm39) Y32* probably null Het
Atp9b A G 18: 80,961,041 (GRCm39) S57P Het
Atr G T 9: 95,744,844 (GRCm39) E54* probably null Het
Bace1 A G 9: 45,767,393 (GRCm39) D192G probably benign Het
Bltp1 A T 3: 37,004,162 (GRCm39) T1624S probably benign Het
Bltp3b T C 10: 89,615,744 (GRCm39) V129A probably damaging Het
Cd177 G T 7: 24,456,072 (GRCm39) T232K probably damaging Het
Chil4 T A 3: 106,111,475 (GRCm39) D213V probably damaging Het
Cmya5 A T 13: 93,182,546 (GRCm39) I3538N probably damaging Het
Cyp26a1 T A 19: 37,687,753 (GRCm39) M287K possibly damaging Het
Dcaf5 T C 12: 80,446,732 (GRCm39) D129G probably damaging Het
Dnah12 A C 14: 26,536,370 (GRCm39) K2095N probably benign Het
Dnpep G A 1: 75,292,701 (GRCm39) S106L probably damaging Het
Dock2 C T 11: 34,189,675 (GRCm39) E1499K possibly damaging Het
Dus4l A G 12: 31,696,714 (GRCm39) F88L probably damaging Het
Fcrl2 A C 3: 87,166,830 (GRCm39) D54E probably benign Het
Fign T A 2: 63,809,950 (GRCm39) H440L possibly damaging Het
Gabpa A G 16: 84,643,174 (GRCm39) D157G probably damaging Het
Gapdh T A 6: 125,142,403 (GRCm39) probably benign Het
Gbp8 G T 5: 105,164,081 (GRCm39) R406S probably benign Het
Gm21775 A G Y: 10,553,894 (GRCm39) R148G possibly damaging Het
Gm28363 G A 1: 117,626,579 (GRCm39) V6I unknown Het
Gmps A G 3: 63,918,982 (GRCm39) D522G probably damaging Het
Gpr75 T C 11: 30,842,687 (GRCm39) S531P probably damaging Het
Hars2 G T 18: 36,923,614 (GRCm39) E468D probably benign Het
Jph4 C A 14: 55,352,664 (GRCm39) R23L probably damaging Het
Kctd12 T A 14: 103,219,230 (GRCm39) Y216F probably benign Het
L3mbtl1 G A 2: 162,791,460 (GRCm39) probably null Het
Lama4 G A 10: 38,841,729 (GRCm39) probably benign Het
Lyst T A 13: 13,926,675 (GRCm39) S3494T possibly damaging Het
Mybpc2 A G 7: 44,155,617 (GRCm39) S879P probably benign Het
Ncaph C T 2: 126,964,034 (GRCm39) V304M probably benign Het
Noto A T 6: 85,405,047 (GRCm39) I229F possibly damaging Het
Or10n7-ps1 T C 9: 39,597,731 (GRCm39) M170V unknown Het
Or4c29 T C 2: 88,740,203 (GRCm39) D178G probably damaging Het
Or8k25 T A 2: 86,243,695 (GRCm39) K234* probably null Het
Pald1 A T 10: 61,182,845 (GRCm39) V368E probably damaging Het
Pde9a T A 17: 31,678,071 (GRCm39) M217K probably damaging Het
Pira1 A T 7: 3,741,828 (GRCm39) V184E probably damaging Het
Pitpnm2 G T 5: 124,259,366 (GRCm39) A1323E probably benign Het
Ppp1r3a T C 6: 14,719,190 (GRCm39) S575G probably benign Het
Prok1 T C 3: 107,146,941 (GRCm39) I9V probably benign Het
Ptprc A T 1: 137,998,918 (GRCm39) V905D probably damaging Het
Rbm25 G T 12: 83,710,772 (GRCm39) G295V unknown Het
Rreb1 T C 13: 38,100,544 (GRCm39) M225T possibly damaging Het
Ryr3 T C 2: 112,858,989 (GRCm39) K55E probably damaging Het
Saxo4 T A 19: 10,459,702 (GRCm39) M2L probably benign Het
Scgb2b26 G T 7: 33,644,379 (GRCm39) T4K probably damaging Het
Setx C A 2: 29,038,184 (GRCm39) D1556E probably benign Het
Sft2d1 C T 17: 8,542,164 (GRCm39) T136I possibly damaging Het
Sirt5 C T 13: 43,525,380 (GRCm39) A63V possibly damaging Het
Skor2 A G 18: 76,947,504 (GRCm39) T409A possibly damaging Het
Slc12a6 T C 2: 112,164,760 (GRCm39) M153T probably benign Het
Slc34a1 A G 13: 24,006,348 (GRCm39) Y458C probably damaging Het
Slc36a2 A G 11: 55,053,483 (GRCm39) V385A possibly damaging Het
St6galnac5 A T 3: 152,552,131 (GRCm39) H145Q probably damaging Het
Tal1 T A 4: 114,925,610 (GRCm39) N226K probably damaging Het
Tgtp2 G C 11: 48,950,135 (GRCm39) R146G probably damaging Het
Usp6nl T C 2: 6,445,330 (GRCm39) S436P probably benign Het
Utp3 A G 5: 88,702,621 (GRCm39) E50G probably benign Het
Zfp12 A T 5: 143,225,749 (GRCm39) Q19L probably damaging Het
Other mutations in Cacna1d
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00494:Cacna1d APN 14 29,818,907 (GRCm39) missense probably damaging 0.97
IGL00857:Cacna1d APN 14 30,072,638 (GRCm39) missense possibly damaging 0.83
IGL01015:Cacna1d APN 14 29,773,699 (GRCm39) splice site probably benign
IGL01420:Cacna1d APN 14 29,773,595 (GRCm39) missense probably benign 0.01
IGL01470:Cacna1d APN 14 29,821,099 (GRCm39) missense probably damaging 0.99
IGL01560:Cacna1d APN 14 29,821,163 (GRCm39) missense probably benign 0.00
IGL01617:Cacna1d APN 14 29,824,328 (GRCm39) missense probably damaging 1.00
IGL01820:Cacna1d APN 14 29,764,823 (GRCm39) missense possibly damaging 0.79
IGL01948:Cacna1d APN 14 29,846,751 (GRCm39) missense probably damaging 1.00
IGL02702:Cacna1d APN 14 29,845,490 (GRCm39) nonsense probably null
IGL02864:Cacna1d APN 14 29,773,663 (GRCm39) missense probably benign 0.10
IGL03082:Cacna1d APN 14 29,821,190 (GRCm39) missense probably damaging 1.00
Brisk UTSW 14 29,893,271 (GRCm39) missense possibly damaging 0.91
Troppo UTSW 14 29,845,411 (GRCm39) missense probably damaging 1.00
PIT4651001:Cacna1d UTSW 14 29,900,602 (GRCm39) missense probably damaging 1.00
R0015:Cacna1d UTSW 14 29,836,928 (GRCm39) missense probably benign 0.00
R0015:Cacna1d UTSW 14 29,836,928 (GRCm39) missense probably benign 0.00
R0033:Cacna1d UTSW 14 29,827,446 (GRCm39) missense probably damaging 0.99
R0047:Cacna1d UTSW 14 30,068,747 (GRCm39) splice site probably benign
R0047:Cacna1d UTSW 14 30,068,747 (GRCm39) splice site probably benign
R0051:Cacna1d UTSW 14 29,833,052 (GRCm39) missense probably damaging 1.00
R0051:Cacna1d UTSW 14 29,833,052 (GRCm39) missense probably damaging 1.00
R0067:Cacna1d UTSW 14 29,796,967 (GRCm39) unclassified probably benign
R0067:Cacna1d UTSW 14 29,796,967 (GRCm39) unclassified probably benign
R0238:Cacna1d UTSW 14 29,845,453 (GRCm39) missense probably benign 0.29
R0238:Cacna1d UTSW 14 29,845,453 (GRCm39) missense probably benign 0.29
R0239:Cacna1d UTSW 14 29,845,453 (GRCm39) missense probably benign 0.29
R0239:Cacna1d UTSW 14 29,845,453 (GRCm39) missense probably benign 0.29
R0240:Cacna1d UTSW 14 29,818,926 (GRCm39) missense probably benign 0.00
R0240:Cacna1d UTSW 14 29,818,926 (GRCm39) missense probably benign 0.00
R0284:Cacna1d UTSW 14 29,794,062 (GRCm39) missense probably damaging 1.00
R0416:Cacna1d UTSW 14 29,822,645 (GRCm39) splice site probably benign
R0427:Cacna1d UTSW 14 30,068,774 (GRCm39) missense probably damaging 0.99
R0517:Cacna1d UTSW 14 29,901,232 (GRCm39) missense probably damaging 1.00
R0639:Cacna1d UTSW 14 29,893,251 (GRCm39) critical splice donor site probably null
R0727:Cacna1d UTSW 14 29,852,072 (GRCm39) critical splice donor site probably null
R0732:Cacna1d UTSW 14 29,764,877 (GRCm39) missense probably damaging 0.99
R0843:Cacna1d UTSW 14 29,846,828 (GRCm39) missense probably damaging 1.00
R0900:Cacna1d UTSW 14 29,833,039 (GRCm39) missense probably damaging 1.00
R1278:Cacna1d UTSW 14 29,900,660 (GRCm39) missense probably damaging 1.00
R1340:Cacna1d UTSW 14 29,794,024 (GRCm39) missense probably damaging 0.96
R1527:Cacna1d UTSW 14 29,829,753 (GRCm39) missense probably damaging 1.00
R1711:Cacna1d UTSW 14 29,788,013 (GRCm39) missense probably damaging 1.00
R1736:Cacna1d UTSW 14 29,811,820 (GRCm39) missense probably damaging 1.00
R1763:Cacna1d UTSW 14 29,821,153 (GRCm39) missense probably benign 0.25
R2034:Cacna1d UTSW 14 29,811,820 (GRCm39) missense probably damaging 1.00
R2086:Cacna1d UTSW 14 29,769,314 (GRCm39) missense possibly damaging 0.83
R2126:Cacna1d UTSW 14 29,845,120 (GRCm39) missense probably damaging 1.00
R2218:Cacna1d UTSW 14 29,845,048 (GRCm39) missense probably damaging 1.00
R2219:Cacna1d UTSW 14 29,764,047 (GRCm39) missense probably damaging 1.00
R2262:Cacna1d UTSW 14 30,212,973 (GRCm39) missense possibly damaging 0.46
R2291:Cacna1d UTSW 14 29,764,299 (GRCm39) missense probably damaging 1.00
R2399:Cacna1d UTSW 14 29,774,444 (GRCm39) missense probably benign 0.34
R2424:Cacna1d UTSW 14 29,770,980 (GRCm39) missense probably damaging 0.96
R2568:Cacna1d UTSW 14 29,804,468 (GRCm39) missense probably damaging 0.99
R4038:Cacna1d UTSW 14 29,788,040 (GRCm39) missense probably damaging 0.96
R4509:Cacna1d UTSW 14 29,818,928 (GRCm39) missense probably damaging 1.00
R4649:Cacna1d UTSW 14 29,817,365 (GRCm39) missense probably benign
R4650:Cacna1d UTSW 14 29,817,365 (GRCm39) missense probably benign
R4652:Cacna1d UTSW 14 29,817,365 (GRCm39) missense probably benign
R5009:Cacna1d UTSW 14 29,801,289 (GRCm39) missense probably damaging 1.00
R5058:Cacna1d UTSW 14 29,836,201 (GRCm39) nonsense probably null
R5063:Cacna1d UTSW 14 29,773,340 (GRCm39) missense probably benign
R5138:Cacna1d UTSW 14 30,212,929 (GRCm39) missense probably benign
R5151:Cacna1d UTSW 14 29,845,280 (GRCm39) missense probably damaging 1.00
R5278:Cacna1d UTSW 14 30,074,881 (GRCm39) critical splice donor site probably null
R5286:Cacna1d UTSW 14 30,072,682 (GRCm39) missense possibly damaging 0.69
R5313:Cacna1d UTSW 14 30,068,798 (GRCm39) missense probably benign 0.38
R5383:Cacna1d UTSW 14 29,767,236 (GRCm39) missense possibly damaging 0.51
R5387:Cacna1d UTSW 14 29,822,708 (GRCm39) missense probably damaging 1.00
R5514:Cacna1d UTSW 14 30,072,790 (GRCm39) nonsense probably null
R5524:Cacna1d UTSW 14 29,764,086 (GRCm39) missense probably benign 0.01
R5663:Cacna1d UTSW 14 29,845,297 (GRCm39) missense probably damaging 1.00
R5712:Cacna1d UTSW 14 29,796,954 (GRCm39) missense probably damaging 1.00
R5796:Cacna1d UTSW 14 29,788,073 (GRCm39) missense probably damaging 1.00
R5906:Cacna1d UTSW 14 29,818,917 (GRCm39) missense probably damaging 1.00
R5923:Cacna1d UTSW 14 29,833,105 (GRCm39) missense probably damaging 1.00
R5936:Cacna1d UTSW 14 29,893,271 (GRCm39) missense possibly damaging 0.91
R5938:Cacna1d UTSW 14 29,825,692 (GRCm39) missense probably damaging 1.00
R6041:Cacna1d UTSW 14 29,764,314 (GRCm39) missense probably damaging 1.00
R6432:Cacna1d UTSW 14 29,845,411 (GRCm39) missense probably damaging 1.00
R6486:Cacna1d UTSW 14 29,836,190 (GRCm39) missense probably benign 0.01
R6600:Cacna1d UTSW 14 29,836,192 (GRCm39) missense probably benign 0.15
R6661:Cacna1d UTSW 14 29,811,832 (GRCm39) missense probably damaging 1.00
R6753:Cacna1d UTSW 14 29,764,743 (GRCm39) missense probably damaging 1.00
R6804:Cacna1d UTSW 14 29,773,622 (GRCm39) missense probably benign 0.00
R6851:Cacna1d UTSW 14 29,764,739 (GRCm39) missense probably damaging 1.00
R6863:Cacna1d UTSW 14 29,797,809 (GRCm39) missense probably damaging 1.00
R6916:Cacna1d UTSW 14 29,817,321 (GRCm39) missense probably damaging 1.00
R6925:Cacna1d UTSW 14 29,773,594 (GRCm39) missense probably benign
R7066:Cacna1d UTSW 14 30,074,935 (GRCm39) intron probably benign
R7242:Cacna1d UTSW 14 29,900,663 (GRCm39) missense probably benign 0.00
R7249:Cacna1d UTSW 14 29,864,660 (GRCm39) missense probably damaging 1.00
R7250:Cacna1d UTSW 14 29,797,108 (GRCm39) missense probably damaging 1.00
R7274:Cacna1d UTSW 14 29,864,600 (GRCm39) missense probably damaging 1.00
R7336:Cacna1d UTSW 14 29,767,239 (GRCm39) missense probably benign 0.18
R7343:Cacna1d UTSW 14 29,845,014 (GRCm39) missense probably benign 0.02
R7411:Cacna1d UTSW 14 30,074,947 (GRCm39) start codon destroyed probably null
R7461:Cacna1d UTSW 14 29,788,120 (GRCm39) missense probably benign 0.05
R7534:Cacna1d UTSW 14 29,801,319 (GRCm39) missense probably damaging 1.00
R7613:Cacna1d UTSW 14 29,788,120 (GRCm39) missense probably benign 0.05
R7661:Cacna1d UTSW 14 29,769,177 (GRCm39) missense probably benign 0.07
R7754:Cacna1d UTSW 14 29,797,809 (GRCm39) missense probably damaging 1.00
R7759:Cacna1d UTSW 14 29,821,145 (GRCm39) missense probably benign 0.01
R7784:Cacna1d UTSW 14 29,845,396 (GRCm39) missense probably damaging 1.00
R7808:Cacna1d UTSW 14 29,833,026 (GRCm39) missense probably damaging 1.00
R7965:Cacna1d UTSW 14 29,769,270 (GRCm39) nonsense probably null
R8225:Cacna1d UTSW 14 29,844,990 (GRCm39) missense probably benign 0.23
R8259:Cacna1d UTSW 14 29,773,475 (GRCm39) missense probably benign
R8348:Cacna1d UTSW 14 29,824,364 (GRCm39) missense probably damaging 1.00
R8448:Cacna1d UTSW 14 29,824,364 (GRCm39) missense probably damaging 1.00
R8822:Cacna1d UTSW 14 29,900,692 (GRCm39) missense probably benign 0.02
R8848:Cacna1d UTSW 14 29,845,283 (GRCm39) missense possibly damaging 0.89
R9122:Cacna1d UTSW 14 29,852,125 (GRCm39) missense probably benign 0.00
R9122:Cacna1d UTSW 14 29,845,402 (GRCm39) missense probably damaging 1.00
R9169:Cacna1d UTSW 14 29,796,873 (GRCm39) missense probably damaging 1.00
R9199:Cacna1d UTSW 14 29,764,893 (GRCm39) missense probably benign 0.26
R9203:Cacna1d UTSW 14 29,773,669 (GRCm39) missense probably benign 0.04
R9263:Cacna1d UTSW 14 29,796,925 (GRCm39) missense probably damaging 1.00
R9346:Cacna1d UTSW 14 29,818,880 (GRCm39) missense possibly damaging 0.86
R9444:Cacna1d UTSW 14 29,829,741 (GRCm39) critical splice donor site probably null
R9487:Cacna1d UTSW 14 29,845,419 (GRCm39) missense possibly damaging 0.90
R9542:Cacna1d UTSW 14 29,845,316 (GRCm39) missense probably benign 0.00
R9651:Cacna1d UTSW 14 29,764,881 (GRCm39) missense probably benign 0.00
R9785:Cacna1d UTSW 14 29,824,300 (GRCm39) critical splice donor site probably null
Z1176:Cacna1d UTSW 14 29,833,073 (GRCm39) missense probably benign 0.15
Z1176:Cacna1d UTSW 14 29,901,145 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- GGCTAAGGCTCTACTCTAGAAGG -3'
(R):5'- GTGCCCCTTTCTATCAGTGG -3'

Sequencing Primer
(F):5'- AGGCTCTACTCTAGAAGGTTGTTTTC -3'
(R):5'- ATCAGTGGACAGTATTGTTGTCTCCC -3'
Posted On 2019-06-26