Incidental Mutation 'R1745:Capn3'
ID 193905
Institutional Source Beutler Lab
Gene Symbol Capn3
Ensembl Gene ENSMUSG00000079110
Gene Name calpain 3
Synonyms Capa3, Lp82, Capa-3, p94
MMRRC Submission 039777-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.221) question?
Stock # R1745 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 120294074-120335400 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 120320170 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Methionine at position 283 (V283M)
Ref Sequence ENSEMBL: ENSMUSP00000087482 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028748] [ENSMUST00000028749] [ENSMUST00000090028] [ENSMUST00000110716] [ENSMUST00000110719] [ENSMUST00000110721]
AlphaFold Q64691
Predicted Effect possibly damaging
Transcript: ENSMUST00000028748
AA Change: V283M

PolyPhen 2 Score 0.867 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000028748
Gene: ENSMUSG00000079110
AA Change: V283M

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 possibly damaging
Transcript: ENSMUST00000028749
AA Change: V351M

PolyPhen 2 Score 0.638 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000028749
Gene: ENSMUSG00000079110
AA Change: V351M

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 possibly damaging
Transcript: ENSMUST00000090028
AA Change: V283M

PolyPhen 2 Score 0.867 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000087482
Gene: ENSMUSG00000079110
AA Change: V283M

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: V331M

PolyPhen 2 Score 0.790 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000106344
Gene: ENSMUSG00000079110
AA Change: V331M

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 possibly damaging
Transcript: ENSMUST00000110719
AA Change: V331M

PolyPhen 2 Score 0.672 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000106347
Gene: ENSMUSG00000079110
AA Change: V331M

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 possibly damaging
Transcript: ENSMUST00000110721
AA Change: V303M

PolyPhen 2 Score 0.600 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000106349
Gene: ENSMUSG00000079110
AA Change: V303M

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: ENSMUST00000124129
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139336
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145993
Meta Mutation Damage Score 0.2991 question?
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.9%
  • 10x: 95.3%
  • 20x: 92.5%
Validation Efficiency 98% (54/55)
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc10 A T 17: 46,623,359 (GRCm39) V851E probably benign Het
Adam28 A G 14: 68,870,620 (GRCm39) I351T probably benign Het
Agrp G T 8: 106,293,467 (GRCm39) T106K probably damaging Het
Anpep C T 7: 79,488,004 (GRCm39) E518K probably benign Het
Ap2a1 T C 7: 44,556,369 (GRCm39) E285G probably damaging Het
Arfgef1 A C 1: 10,243,480 (GRCm39) I1023R probably damaging Het
Atp2c2 G A 8: 120,451,833 (GRCm39) V133I probably benign Het
Bpifb6 A G 2: 153,753,403 (GRCm39) T401A possibly damaging Het
Chd6 A T 2: 160,823,587 (GRCm39) V1261E probably damaging Het
Col22a1 C T 15: 71,878,636 (GRCm39) A174T probably damaging Het
Crnn T C 3: 93,054,198 (GRCm39) V27A probably benign Het
Dclk2 C T 3: 86,712,946 (GRCm39) R503Q possibly damaging Het
Dgkd T C 1: 87,859,766 (GRCm39) probably null Het
Diaph3 A G 14: 87,203,996 (GRCm39) L554P probably damaging Het
Ephb4 A T 5: 137,358,696 (GRCm39) H293L probably benign Het
Erbin G T 13: 103,975,957 (GRCm39) H646N probably damaging Het
Faiml T C 9: 99,116,511 (GRCm39) N60D probably benign Het
Fem1al A G 11: 29,774,723 (GRCm39) S245P probably benign Het
Flot1 A G 17: 36,135,552 (GRCm39) E102G probably damaging Het
Fryl G A 5: 73,190,204 (GRCm39) probably benign Het
Gad1-ps A T 10: 99,281,386 (GRCm39) noncoding transcript Het
Gtf3c3 A G 1: 54,473,371 (GRCm39) S81P probably damaging Het
Hs1bp3 C T 12: 8,371,690 (GRCm39) Q91* probably null Het
Igf1r T C 7: 67,819,661 (GRCm39) C324R probably damaging Het
Il23r G A 6: 67,443,275 (GRCm39) T276I probably damaging Het
Ip6k1 G A 9: 107,918,195 (GRCm39) E77K possibly damaging Het
Kctd1 A T 18: 15,196,263 (GRCm39) probably benign Het
Kmt2b A T 7: 30,285,275 (GRCm39) M539K possibly damaging Het
Man2b1 T A 8: 85,820,563 (GRCm39) F617I probably damaging Het
Med15 G A 16: 17,473,570 (GRCm39) probably benign Het
Myo9b A G 8: 71,806,691 (GRCm39) K1543R probably damaging Het
N4bp2 A G 5: 65,948,165 (GRCm39) Y265C probably benign Het
N4bp2l2 A T 5: 150,585,424 (GRCm39) N185K probably benign Het
Nkx2-1 A G 12: 56,580,529 (GRCm39) M137T probably benign Het
Or51q1c A G 7: 103,653,270 (GRCm39) T269A probably benign Het
Prickle2 A T 6: 92,353,574 (GRCm39) Y631N probably damaging Het
Ptpro A G 6: 137,377,643 (GRCm39) T698A probably benign Het
Rapgef3 T C 15: 97,648,059 (GRCm39) I690V probably benign Het
Rnf44 G A 13: 54,830,005 (GRCm39) R271W probably damaging Het
Rundc3a GAGCC GAGCCAGCC 11: 102,291,739 (GRCm39) probably null Het
Ryr2 A G 13: 11,805,153 (GRCm39) Y904H probably damaging Het
Suz12 T C 11: 79,912,922 (GRCm39) L322P probably damaging Het
Tnfsf13 G A 11: 69,575,973 (GRCm39) A38V probably benign Het
Topbp1 G A 9: 103,186,044 (GRCm39) R62H probably benign Het
Tor1aip1 G T 1: 155,906,180 (GRCm39) probably null Het
Trpv4 A T 5: 114,771,215 (GRCm39) V438E probably damaging Het
Tsku A T 7: 98,001,386 (GRCm39) V315E possibly damaging Het
Ttc38 T C 15: 85,717,373 (GRCm39) L16P probably damaging Het
Vmn1r170 A G 7: 23,305,759 (GRCm39) I54V probably damaging Het
Vmn1r71 T C 7: 10,482,196 (GRCm39) D98G probably benign Het
Wdfy3 A T 5: 102,096,795 (GRCm39) D334E probably damaging Het
Zfhx3 T A 8: 109,682,494 (GRCm39) F3311Y unknown Het
Zswim9 A G 7: 13,003,482 (GRCm39) S123P probably 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
R1566:Capn3 UTSW 2 120,333,474 (GRCm39) missense possibly damaging 0.72
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'- GCAAGCTTCTGGTTTGTCCACCTG -3'
(R):5'- GCACCATCATGTTCACTGAGTCCC -3'

Sequencing Primer
(F):5'- ATCAGATGCCCCATCTTTCC -3'
(R):5'- TTTTGGGGAACCCACACC -3'
Posted On 2014-05-23