Incidental Mutation 'R1566:Capn3'
ID 175247
Institutional Source Beutler Lab
Gene Symbol Capn3
Ensembl Gene ENSMUSG00000079110
Gene Name calpain 3
Synonyms Capa3, Lp82, Capa-3, p94
MMRRC Submission 039605-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.217) question?
Stock # R1566 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 120294074-120335400 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 120333474 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Serine at position 627 (R627S)
Ref Sequence ENSEMBL: ENSMUSP00000087482 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028748] [ENSMUST00000028749] [ENSMUST00000055241] [ENSMUST00000090028] [ENSMUST00000110716] [ENSMUST00000110719] [ENSMUST00000110721]
AlphaFold Q64691
Predicted Effect probably benign
Transcript: ENSMUST00000028748
AA Change: R599S

PolyPhen 2 Score 0.192 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000028748
Gene: ENSMUSG00000079110
AA Change: R599S

DomainStartEndE-ValueType
CysPc 32 357 5.98e-199 SMART
calpain_III 360 514 4.27e-90 SMART
EFh 584 612 5.53e-4 SMART
EFh 614 642 1.8e-3 SMART
EFh 679 707 4.32e1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000028749
AA Change: R711S

PolyPhen 2 Score 0.123 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000028749
Gene: ENSMUSG00000079110
AA Change: R711S

DomainStartEndE-ValueType
CysPc 56 425 2.09e-212 SMART
calpain_III 428 582 4.27e-90 SMART
Pfam:Calpain_u2 583 653 1.3e-31 PFAM
EFh 696 724 5.53e-4 SMART
EFh 726 754 1.8e-3 SMART
EFh 791 819 4.32e1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000055241
SMART Domains Protein: ENSMUSP00000055602
Gene: ENSMUSG00000027288

DomainStartEndE-ValueType
ZnF_C2H2 5 29 1.51e0 SMART
ZnF_C2H2 43 67 7.18e1 SMART
low complexity region 75 92 N/A INTRINSIC
low complexity region 141 152 N/A INTRINSIC
low complexity region 199 212 N/A INTRINSIC
low complexity region 466 480 N/A INTRINSIC
coiled coil region 800 823 N/A INTRINSIC
low complexity region 842 856 N/A INTRINSIC
low complexity region 1049 1062 N/A INTRINSIC
low complexity region 1312 1321 N/A INTRINSIC
low complexity region 1361 1373 N/A INTRINSIC
low complexity region 1389 1409 N/A INTRINSIC
WD40 1525 1562 9.24e-4 SMART
WD40 1565 1607 1.83e-7 SMART
PQQ 1587 1618 3.42e2 SMART
WD40 1651 1691 3.45e-1 SMART
PQQ 1671 1702 9.14e1 SMART
WD40 1694 1731 2.12e-3 SMART
PQQ 1711 1742 6.42e0 SMART
WD40 1734 1771 6e-3 SMART
PQQ 1751 1782 5.7e2 SMART
WD40 1774 1811 3.58e-1 SMART
ZnF_C2H2 1818 1843 5.34e-1 SMART
ZnF_C2H2 1851 1879 1.31e2 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000090028
AA Change: R627S

PolyPhen 2 Score 0.721 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000087482
Gene: ENSMUSG00000079110
AA Change: R627S

DomainStartEndE-ValueType
CysPc 32 357 5.98e-199 SMART
calpain_III 360 514 4.27e-90 SMART
low complexity region 585 599 N/A INTRINSIC
EFh 612 640 5.53e-4 SMART
EFh 642 670 1.8e-3 SMART
EFh 707 735 4.32e1 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000110716
AA Change: R647S

PolyPhen 2 Score 0.564 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000106344
Gene: ENSMUSG00000079110
AA Change: R647S

DomainStartEndE-ValueType
CysPc 32 405 8.38e-203 SMART
calpain_III 408 562 4.27e-90 SMART
EFh 632 660 5.53e-4 SMART
EFh 662 690 1.8e-3 SMART
EFh 727 755 4.32e1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000110719
AA Change: R675S

PolyPhen 2 Score 0.047 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000106347
Gene: ENSMUSG00000079110
AA Change: R675S

DomainStartEndE-ValueType
CysPc 32 405 8.38e-203 SMART
calpain_III 408 562 4.27e-90 SMART
low complexity region 633 647 N/A INTRINSIC
EFh 660 688 5.53e-4 SMART
EFh 690 718 1.8e-3 SMART
EFh 755 783 4.32e1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000110721
AA Change: R619S

PolyPhen 2 Score 0.057 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000106349
Gene: ENSMUSG00000079110
AA Change: R619S

DomainStartEndE-ValueType
CysPc 56 377 1.13e-208 SMART
calpain_III 380 534 4.27e-90 SMART
EFh 604 632 5.53e-4 SMART
EFh 634 662 1.8e-3 SMART
EFh 699 727 4.32e1 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145993
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151342
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125238
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139336
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124129
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141181
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.1%
  • 10x: 95.7%
  • 20x: 90.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Calpain, a heterodimer consisting of a large and a small subunit, is a major intracellular protease, although its function has not been well established. This gene encodes a muscle-specific member of the calpain large subunit family that specifically binds to titin. Mutations in this gene are associated with limb-girdle muscular dystrophies type 2A. Alternate promoters and alternative splicing result in multiple transcript variants encoding different isoforms and some variants are ubiquitously expressed. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutation of this gene results in muscle dystrophy. The psoas, soleus, and deltoid muscles are the most severely affected. The mutant allele appears to be preferentially transmitted resulting in ratio distortion. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700012B07Rik T A 11: 109,679,632 (GRCm39) I247F probably benign Het
Afap1l1 T C 18: 61,888,714 (GRCm39) N119S probably benign Het
Ap2a1 T C 7: 44,552,904 (GRCm39) D721G probably benign Het
Ap3m2 C T 8: 23,293,967 (GRCm39) V28M probably damaging Het
Arhgef7 A G 8: 11,832,620 (GRCm39) T32A possibly damaging Het
Avl9 C T 6: 56,713,467 (GRCm39) R242* probably null Het
Bsn G A 9: 108,003,184 (GRCm39) T407I probably benign Het
Car13 G A 3: 14,715,758 (GRCm39) R92Q probably benign Het
Clcn1 T C 6: 42,268,374 (GRCm39) I149T possibly damaging Het
Col1a2 G T 6: 4,523,613 (GRCm39) G514V probably damaging Het
Ctsw C A 19: 5,515,445 (GRCm39) C347F probably damaging Het
Dna2 C T 10: 62,784,966 (GRCm39) R28W probably benign Het
Eif1ad8 A T 12: 87,564,001 (GRCm39) H112L probably benign Het
Eml1 T A 12: 108,438,151 (GRCm39) V97D probably damaging Het
Epb41l1 A G 2: 156,363,879 (GRCm39) E796G probably benign Het
Gdnf A G 15: 7,863,895 (GRCm39) K102R probably benign Het
Gm1110 T C 9: 26,792,166 (GRCm39) E618G probably damaging Het
Gmnc T C 16: 26,782,689 (GRCm39) D22G probably damaging Het
Greb1 T C 12: 16,761,829 (GRCm39) D517G possibly damaging Het
Gsta1 A T 9: 78,149,741 (GRCm39) K185* probably null Het
Ift88 A G 14: 57,678,468 (GRCm39) D160G probably benign Het
Intu T A 3: 40,647,008 (GRCm39) I627N probably damaging Het
Itgav T A 2: 83,566,974 (GRCm39) F101L probably damaging Het
Kars1 C T 8: 112,724,290 (GRCm39) V475I probably benign Het
Klra3 G C 6: 130,310,107 (GRCm39) R138G probably benign Het
Klra7 A G 6: 130,208,564 (GRCm39) V6A probably damaging Het
Krtap6-2 A G 16: 89,216,626 (GRCm39) S114P unknown Het
Ldlrad4 T C 18: 68,383,669 (GRCm39) S122P probably benign Het
Lig4 C A 8: 10,023,650 (GRCm39) L43F probably benign Het
Mfsd4a T C 1: 131,986,917 (GRCm39) D137G probably damaging Het
Mmel1 C T 4: 154,968,110 (GRCm39) R149C probably damaging Het
Morc2b T A 17: 33,355,948 (GRCm39) H608L probably benign Het
Mrgpra6 G A 7: 46,838,652 (GRCm39) T182I probably benign Het
Nat8l C A 5: 34,158,200 (GRCm39) N203K probably benign Het
Nin A T 12: 70,101,253 (GRCm39) V448E probably damaging Het
Or10a4 T G 7: 106,696,759 (GRCm39) F29C probably damaging Het
Or2m12 T A 16: 19,105,077 (GRCm39) M139L possibly damaging Het
Or5k15 T A 16: 58,709,903 (GRCm39) I227F probably damaging Het
Or8k21 G A 2: 86,145,129 (GRCm39) T167I probably benign Het
Pank4 T C 4: 155,064,978 (GRCm39) L759P probably damaging Het
Pcm1 T A 8: 41,743,810 (GRCm39) N1152K probably damaging Het
Pitpnm3 A T 11: 71,949,785 (GRCm39) probably null Het
Plekhg3 T C 12: 76,618,839 (GRCm39) M497T possibly damaging Het
Ppfia3 T C 7: 44,990,112 (GRCm39) D1138G probably damaging Het
Prl6a1 T A 13: 27,499,410 (GRCm39) S59R possibly damaging Het
Pth2r A G 1: 65,427,697 (GRCm39) S457G possibly damaging Het
Rbm25 T A 12: 83,721,828 (GRCm39) N671K probably damaging Het
Rbm26 T A 14: 105,397,980 (GRCm39) K47N unknown Het
Ryr1 T A 7: 28,791,600 (GRCm39) I1435F possibly damaging Het
Scin T A 12: 40,131,673 (GRCm39) H287L probably benign Het
Serpinb9e T C 13: 33,437,477 (GRCm39) L120P probably damaging Het
Slc34a1 A C 13: 55,559,844 (GRCm39) probably null Het
Slc39a10 A G 1: 46,875,245 (GRCm39) F19S possibly damaging Het
Sos1 A G 17: 80,761,345 (GRCm39) V117A probably damaging Het
Spta1 C A 1: 174,012,272 (GRCm39) N359K probably benign Het
Sspo G A 6: 48,443,804 (GRCm39) probably null Het
Stx5a T A 19: 8,719,675 (GRCm39) D13E probably damaging Het
Supt16 G A 14: 52,414,112 (GRCm39) A489V probably damaging Het
Tap1 T A 17: 34,408,520 (GRCm39) L253Q probably benign Het
Tmc6 A G 11: 117,660,262 (GRCm39) S659P probably damaging Het
Tnfsf14 T C 17: 57,500,876 (GRCm39) D65G probably benign Het
Ttc28 G A 5: 111,373,543 (GRCm39) S962N probably damaging Het
Ugt8a T C 3: 125,669,207 (GRCm39) Y299C probably damaging Het
Upk1a A G 7: 30,309,145 (GRCm39) V59A possibly damaging Het
Usp38 T C 8: 81,711,432 (GRCm39) T868A probably benign Het
Wdsub1 G A 2: 59,707,059 (GRCm39) H58Y probably damaging Het
Zc3h7b T C 15: 81,653,035 (GRCm39) S19P possibly damaging Het
Zfp385b A C 2: 77,246,257 (GRCm39) F257V probably benign Het
Zmym4 A C 4: 126,804,940 (GRCm39) I188S possibly damaging Het
Other mutations in Capn3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00543:Capn3 APN 2 120,316,963 (GRCm39) intron probably benign
IGL00976:Capn3 APN 2 120,322,382 (GRCm39) missense possibly damaging 0.81
IGL01538:Capn3 APN 2 120,332,667 (GRCm39) splice site probably null
IGL01564:Capn3 APN 2 120,311,189 (GRCm39) missense probably damaging 1.00
IGL02527:Capn3 APN 2 120,334,966 (GRCm39) missense probably damaging 0.99
IGL02605:Capn3 APN 2 120,326,518 (GRCm39) missense probably damaging 0.98
IGL02678:Capn3 APN 2 120,333,479 (GRCm39) missense probably damaging 1.00
IGL02899:Capn3 APN 2 120,322,382 (GRCm39) missense possibly damaging 0.81
IGL03255:Capn3 APN 2 120,320,189 (GRCm39) missense probably damaging 1.00
R0053:Capn3 UTSW 2 120,322,318 (GRCm39) missense possibly damaging 0.95
R0053:Capn3 UTSW 2 120,322,318 (GRCm39) missense possibly damaging 0.95
R0096:Capn3 UTSW 2 120,333,010 (GRCm39) missense possibly damaging 0.94
R0096:Capn3 UTSW 2 120,333,010 (GRCm39) missense possibly damaging 0.94
R0276:Capn3 UTSW 2 120,318,546 (GRCm39) splice site probably benign
R0601:Capn3 UTSW 2 120,333,077 (GRCm39) splice site probably null
R0714:Capn3 UTSW 2 120,322,361 (GRCm39) missense probably benign 0.32
R1217:Capn3 UTSW 2 120,316,902 (GRCm39) nonsense probably null
R1530:Capn3 UTSW 2 120,312,689 (GRCm39) missense probably damaging 1.00
R1745:Capn3 UTSW 2 120,320,170 (GRCm39) missense possibly damaging 0.87
R1748:Capn3 UTSW 2 120,327,494 (GRCm39) missense probably benign 0.10
R1861:Capn3 UTSW 2 120,316,963 (GRCm39) intron probably benign
R1960:Capn3 UTSW 2 120,294,421 (GRCm39) missense probably benign 0.00
R1971:Capn3 UTSW 2 120,311,228 (GRCm39) missense possibly damaging 0.95
R1994:Capn3 UTSW 2 120,326,418 (GRCm39) missense probably damaging 1.00
R2043:Capn3 UTSW 2 120,322,382 (GRCm39) missense possibly damaging 0.81
R2254:Capn3 UTSW 2 120,331,732 (GRCm39) missense probably benign 0.01
R2255:Capn3 UTSW 2 120,331,732 (GRCm39) missense probably benign 0.01
R3738:Capn3 UTSW 2 120,315,768 (GRCm39) missense possibly damaging 0.85
R3824:Capn3 UTSW 2 120,314,964 (GRCm39) splice site probably benign
R4796:Capn3 UTSW 2 120,333,479 (GRCm39) missense probably damaging 1.00
R5073:Capn3 UTSW 2 120,322,301 (GRCm39) missense probably damaging 1.00
R5116:Capn3 UTSW 2 120,315,773 (GRCm39) missense probably benign 0.00
R5152:Capn3 UTSW 2 120,331,811 (GRCm39) intron probably benign
R5420:Capn3 UTSW 2 120,325,777 (GRCm39) intron probably benign
R5478:Capn3 UTSW 2 120,294,666 (GRCm39) splice site probably null
R5506:Capn3 UTSW 2 120,332,901 (GRCm39) missense probably damaging 0.97
R5664:Capn3 UTSW 2 120,307,506 (GRCm39) missense probably benign 0.04
R5733:Capn3 UTSW 2 120,315,075 (GRCm39) nonsense probably null
R6212:Capn3 UTSW 2 120,307,667 (GRCm39) missense probably benign 0.17
R7176:Capn3 UTSW 2 120,334,973 (GRCm39) missense possibly damaging 0.46
R7219:Capn3 UTSW 2 120,333,935 (GRCm39) missense probably damaging 0.99
R7365:Capn3 UTSW 2 120,325,295 (GRCm39) missense probably damaging 0.98
R7819:Capn3 UTSW 2 120,294,646 (GRCm39) missense probably benign 0.05
R8052:Capn3 UTSW 2 120,316,867 (GRCm39) missense probably benign
R8834:Capn3 UTSW 2 120,294,534 (GRCm39) missense probably damaging 0.98
R8970:Capn3 UTSW 2 120,294,566 (GRCm39) missense possibly damaging 0.90
R9088:Capn3 UTSW 2 120,321,451 (GRCm39) missense probably benign
R9473:Capn3 UTSW 2 120,326,535 (GRCm39) nonsense probably null
R9512:Capn3 UTSW 2 120,326,535 (GRCm39) missense probably damaging 0.99
R9663:Capn3 UTSW 2 120,316,859 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- AGCTGTAAAGCTGGCAGGAACTC -3'
(R):5'- TGCATCATTGACTGCATTTCGCATC -3'

Sequencing Primer
(F):5'- CTGGCAGGAACTCTGGTTAAG -3'
(R):5'- GACTGCATTTCGCATCTCATAG -3'
Posted On 2014-04-24