Incidental Mutation 'R0015:Cacna1d'
ID 19089
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 038310-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.900) question?
Stock # R0015 (G1)
Quality Score
Status Validated
Chromosome 14
Chromosomal Location 29761898-30213113 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 29836928 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 804 (T804I)
Ref Sequence ENSEMBL: ENSMUSP00000153293 (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: T804I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000107868
Gene: ENSMUSG00000015968
AA Change: T804I

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: T826I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000107869
Gene: ENSMUSG00000015968
AA Change: T826I

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: T804I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224073
Predicted Effect probably benign
Transcript: ENSMUST00000224198
AA Change: T824I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
Predicted Effect probably benign
Transcript: ENSMUST00000224395
Predicted Effect probably benign
Transcript: ENSMUST00000224785
AA Change: T804I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Meta Mutation Damage Score 0.0727 question?
Coding Region Coverage
  • 1x: 80.5%
  • 3x: 72.2%
  • 10x: 49.0%
  • 20x: 28.4%
Validation Efficiency 90% (88/98)
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: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A130050O07Rik A G 1: 137,856,394 (GRCm39) Y23C unknown Het
Aadat C T 8: 60,987,605 (GRCm39) probably benign Het
Adcy3 G A 12: 4,245,260 (GRCm39) probably null Het
Armc3 A G 2: 19,301,132 (GRCm39) probably null Het
Astn2 T G 4: 66,184,619 (GRCm39) probably null Het
Borcs8 T C 8: 70,593,017 (GRCm39) probably benign Het
Card19 A G 13: 49,361,532 (GRCm39) L33P probably benign Het
Ccny A C 18: 9,316,682 (GRCm39) probably benign Het
Cdh5 C T 8: 104,867,559 (GRCm39) T612I probably benign Het
Cfap58 A G 19: 48,017,539 (GRCm39) M800V probably benign Het
Clrn1 A T 3: 58,753,848 (GRCm39) I171K probably damaging Het
Cnp T A 11: 100,469,734 (GRCm39) probably null Het
Col12a1 T C 9: 79,558,667 (GRCm39) T1933A probably damaging Het
Cplane1 G A 15: 8,215,668 (GRCm39) R408H probably damaging Het
Cwf19l2 A G 9: 3,454,666 (GRCm39) S660G probably benign Het
Dync1i2 C A 2: 71,044,828 (GRCm39) R13S probably damaging Het
Fat4 T A 3: 39,036,652 (GRCm39) S3435T probably damaging Het
Fchsd1 A G 18: 38,096,012 (GRCm39) C533R probably benign Het
Fstl5 G A 3: 76,229,498 (GRCm39) V100M probably damaging Het
Gria2 C T 3: 80,615,074 (GRCm39) G469S probably damaging Het
Hsf5 C A 11: 87,548,161 (GRCm39) H615N probably benign Het
Ints2 T C 11: 86,140,113 (GRCm39) T240A probably damaging Het
Kcnn3 A C 3: 89,570,080 (GRCm39) D631A probably damaging Het
Lama4 C T 10: 38,951,432 (GRCm39) T1059M possibly damaging Het
Lgals8 A G 13: 12,462,179 (GRCm39) L226P probably damaging Het
Lonp1 T A 17: 56,925,406 (GRCm39) Q462L probably benign Het
Mark2 A T 19: 7,263,142 (GRCm39) Y231* probably null Het
Mdh1b T C 1: 63,760,959 (GRCm39) probably benign Het
Myh7b C T 2: 155,464,206 (GRCm39) P569L probably damaging Het
Myl3 A C 9: 110,596,997 (GRCm39) D119A probably damaging Het
Ncapd3 C A 9: 26,963,105 (GRCm39) A470E probably damaging Het
Ndrg2 A G 14: 52,147,902 (GRCm39) probably benign Het
Nprl2 A T 9: 107,421,618 (GRCm39) I209F probably damaging Het
Pcf11 T A 7: 92,307,525 (GRCm39) H881L probably benign Het
Pde10a A G 17: 9,196,029 (GRCm39) D640G probably damaging Het
Pdxdc1 A T 16: 13,705,547 (GRCm39) probably benign Het
Polr2g A G 19: 8,771,016 (GRCm39) I160T probably damaging Het
Pter G A 2: 13,005,811 (GRCm39) G328D probably damaging Het
Rad51 T A 2: 118,946,808 (GRCm39) M5K probably benign Het
Rbm43 T A 2: 51,815,679 (GRCm39) I181F probably benign Het
Rgs12 T C 5: 35,180,120 (GRCm39) probably benign Het
Slc20a2 C A 8: 23,025,361 (GRCm39) A21E probably damaging Het
Sybu T C 15: 44,536,896 (GRCm39) R349G probably damaging Het
Tmem161b C A 13: 84,370,533 (GRCm39) probably null Het
Xirp2 C A 2: 67,341,243 (GRCm39) Y1161* probably null Het
Zfand4 C A 6: 116,305,258 (GRCm39) T705K 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
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
R7188:Cacna1d UTSW 14 29,811,790 (GRCm39) missense 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
Posted On 2013-03-25