Mutagenetix > Incidental Mutation

Incidental Mutation 'R1971:Capn3'

220797

Institutional Source

Beutler Lab

Gene Symbol

Capn3

Ensembl Gene

ENSMUSG00000079110

Gene Name

calpain 3

Synonyms

Capa3, Lp82, Capa-3, p94

MMRRC Submission

039984-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.221) question?

Stock #

R1971 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

120294074-120335400 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 120311228 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 105 (D105G)

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: D105G

PolyPhen 2 Score 0.846 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000028748
Gene: ENSMUSG00000079110
AA Change: D105G

Domain	Start	End	E-Value	Type
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: D125G

PolyPhen 2 Score 0.515 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000028749
Gene: ENSMUSG00000079110
AA Change: D125G

Domain	Start	End	E-Value	Type
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: D105G

PolyPhen 2 Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000087482
Gene: ENSMUSG00000079110
AA Change: D105G

Domain	Start	End	E-Value	Type
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: D105G

PolyPhen 2 Score 0.846 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000106344
Gene: ENSMUSG00000079110
AA Change: D105G

Domain	Start	End	E-Value	Type
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: D105G

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000106347
Gene: ENSMUSG00000079110
AA Change: D105G

Domain	Start	End	E-Value	Type
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: D125G

PolyPhen 2 Score 0.515 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000106349
Gene: ENSMUSG00000079110
AA Change: D125G

Domain	Start	End	E-Value	Type
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: ENSMUST00000145993

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151924

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139336

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.3%

Validation Efficiency

99% (115/116)

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: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700001O22Rik	A	T	2: 30,686,566 (GRCm39)	I242N	probably benign	Het
2510009E07Rik	G	T	16: 21,472,048 (GRCm39)	Y217*	probably null	Het
4931429L15Rik	C	T	9: 46,220,086 (GRCm39)	V149M	probably benign	Het
Abcg8	G	T	17: 85,002,587 (GRCm39)		probably benign	Het
Acox1	A	G	11: 116,089,087 (GRCm39)	F77S	probably benign	Het
Adgrb3	G	T	1: 25,586,525 (GRCm39)	H389Q	probably benign	Het
Ak7	A	G	12: 105,692,504 (GRCm39)	N186S	probably damaging	Het
Apobr	A	G	7: 126,185,397 (GRCm39)	T303A	probably benign	Het
Arnt	C	T	3: 95,355,704 (GRCm39)	S16L	possibly damaging	Het
Bcl9l	T	C	9: 44,419,996 (GRCm39)		probably null	Het
Bco2	T	C	9: 50,457,284 (GRCm39)	D86G	probably damaging	Het
Bmpr1b	T	A	3: 141,563,333 (GRCm39)	I204F	probably damaging	Het
Bpifb5	C	A	2: 154,072,264 (GRCm39)	Q324K	probably benign	Het
Cacna2d2	G	A	9: 107,389,205 (GRCm39)	V223I	probably damaging	Het
Ccdc40	G	T	11: 119,153,901 (GRCm39)		probably null	Het
Ccdc83	T	A	7: 89,893,362 (GRCm39)	S132C	probably damaging	Het
Ckap2l	A	G	2: 129,127,342 (GRCm39)	S279P	possibly damaging	Het
Cldn12	C	A	5: 5,558,137 (GRCm39)	A97S	probably benign	Het
Clec2l	T	G	6: 38,640,309 (GRCm39)	S47A	probably benign	Het
Csnk1d	C	A	11: 120,863,274 (GRCm39)	R222M	possibly damaging	Het
Ctnna1	T	A	18: 35,287,580 (GRCm39)	D96E	probably benign	Het
D630045J12Rik	T	C	6: 38,145,078 (GRCm39)	D1316G	probably damaging	Het
Ddx4	C	T	13: 112,736,547 (GRCm39)	V608I	probably damaging	Het
Dmtf1	T	C	5: 9,198,989 (GRCm39)	E48G	probably benign	Het
Dnah17	G	C	11: 117,995,361 (GRCm39)	Q996E	probably benign	Het
Dnah9	G	C	11: 65,739,197 (GRCm39)	N4180K	probably damaging	Het
Dpf3	T	A	12: 83,371,809 (GRCm39)		probably null	Het
Drd2	T	C	9: 49,318,359 (GRCm39)	F434L	probably damaging	Het
En1	A	G	1: 120,534,742 (GRCm39)	T344A	unknown	Het
Eri3	A	G	4: 117,421,964 (GRCm39)	T81A	probably benign	Het
Fam20a	T	C	11: 109,576,237 (GRCm39)	Y174C	probably damaging	Het
Fam234a	G	C	17: 26,435,629 (GRCm39)		probably null	Het
Fam76a	A	T	4: 132,631,294 (GRCm39)	I217N	probably damaging	Het
Fancm	T	A	12: 65,148,466 (GRCm39)	S694T	probably benign	Het
Fcgbpl1	C	A	7: 27,830,937 (GRCm39)	A50E	possibly damaging	Het
Foxo3	A	G	10: 42,073,258 (GRCm39)	S420P	probably benign	Het
Foxp4	C	T	17: 48,186,796 (GRCm39)	R378Q	unknown	Het
Gm136	T	G	4: 34,755,986 (GRCm39)	D9A	probably benign	Het
Gstt2	G	T	10: 75,668,499 (GRCm39)	T116N	probably benign	Het
Hs3st6	A	G	17: 24,972,267 (GRCm39)	T70A	probably benign	Het
Hspa14	A	G	2: 3,490,804 (GRCm39)	V461A	possibly damaging	Het
Itih5	A	T	2: 10,243,379 (GRCm39)	D372V	probably damaging	Het
Kcna2	A	T	3: 107,012,140 (GRCm39)	R240S	probably damaging	Het
Kctd18	T	C	1: 58,006,779 (GRCm39)	I24V	probably benign	Het
Lap3	T	C	5: 45,663,508 (GRCm39)		probably benign	Het
Lcp1	T	C	14: 75,437,946 (GRCm39)	S119P	probably damaging	Het
Lig3	G	C	11: 82,686,544 (GRCm39)	D642H	probably benign	Het
Lpin1	A	T	12: 16,630,724 (GRCm39)	L58H	probably damaging	Het
Map4k5	G	T	12: 69,873,102 (GRCm39)	P468Q	possibly damaging	Het
Med31	G	A	11: 72,106,244 (GRCm39)		probably benign	Het
Mki67	A	T	7: 135,315,688 (GRCm39)		probably null	Het
Mrc1	G	A	2: 14,249,103 (GRCm39)		probably null	Het
Msh3	A	G	13: 92,359,784 (GRCm39)	I16T	probably damaging	Het
Msh3	T	A	13: 92,386,328 (GRCm39)		probably benign	Het
Mst1r	A	T	9: 107,790,411 (GRCm39)	I675F	probably benign	Het
Myb	A	C	10: 21,016,555 (GRCm39)	S652A	probably benign	Het
Myh2	G	T	11: 67,080,004 (GRCm39)	S1099I	possibly damaging	Het
Myl6b	A	G	10: 128,330,512 (GRCm39)	V181A	probably damaging	Het
Myt1l	A	T	12: 29,877,091 (GRCm39)	K247N	unknown	Het
Nanos2	G	T	7: 18,721,629 (GRCm39)	V34L	probably benign	Het
Nav1	T	C	1: 135,460,091 (GRCm39)	T411A	probably benign	Het
Nedd9	T	A	13: 41,492,424 (GRCm39)	I23F	probably damaging	Het
Nes	G	A	3: 87,885,634 (GRCm39)	V1254I	possibly damaging	Het
Nol6	A	G	4: 41,119,542 (GRCm39)	F588S	probably damaging	Het
Numa1	C	T	7: 101,658,529 (GRCm39)	A1605V	probably damaging	Het
Ofd1	T	C	X: 165,210,210 (GRCm39)	Y205C	probably benign	Het
Olr1	T	C	6: 129,470,498 (GRCm39)	E223G	probably benign	Het
Or1e30	T	A	11: 73,678,616 (GRCm39)	M284K	probably damaging	Het
Or2ag12	T	A	7: 106,276,877 (GRCm39)	N272I	probably damaging	Het
Or4c118	A	T	2: 88,975,078 (GRCm39)	C96*	probably null	Het
Or51k2	A	T	7: 103,596,150 (GRCm39)	I126F	probably damaging	Het
Or51l4	C	T	7: 103,404,527 (GRCm39)	W88*	probably null	Het
Pate6	T	A	9: 35,700,309 (GRCm39)	H92L	probably benign	Het
Pclo	A	G	5: 14,763,487 (GRCm39)	T3987A	unknown	Het
Pik3cg	A	T	12: 32,242,152 (GRCm39)	V986D	probably damaging	Het
Pitpnm1	T	A	19: 4,162,450 (GRCm39)	D1093E	probably damaging	Het
Ppp1r12b	T	C	1: 134,793,651 (GRCm39)	D571G	probably benign	Het
Rfx1	A	G	8: 84,822,126 (GRCm39)	E875G	probably damaging	Het
Rnf145	T	A	11: 44,439,642 (GRCm39)	I146N	probably damaging	Het
Rttn	G	A	18: 89,108,557 (GRCm39)	R1587H	probably benign	Het
Safb	A	G	17: 56,912,821 (GRCm39)	H883R	probably benign	Het
Sdhb	A	G	4: 140,700,260 (GRCm39)	D120G	possibly damaging	Het
Serpine3	A	G	14: 62,902,533 (GRCm39)	N48S	probably damaging	Het
Sgms1	T	A	19: 32,137,357 (GRCm39)	I70L	probably benign	Het
Slc1a7	G	T	4: 107,825,782 (GRCm39)	D14Y	probably benign	Het
Smtnl2	C	T	11: 72,302,183 (GRCm39)	A93T	probably benign	Het
Srpra	T	C	9: 35,124,834 (GRCm39)		probably null	Het
Taf6l	A	G	19: 8,752,866 (GRCm39)		probably null	Het
Tbc1d10b	A	T	7: 126,807,036 (GRCm39)	V167E	probably benign	Het
Tbc1d9	G	A	8: 83,976,139 (GRCm39)	R566H	probably damaging	Het
Tenm3	A	G	8: 48,689,348 (GRCm39)	Y2080H	probably damaging	Het
Tex14	A	G	11: 87,402,431 (GRCm39)	N506S	probably damaging	Het
Thada	G	T	17: 84,617,470 (GRCm39)	P1349T	probably damaging	Het
Tjp1	G	T	7: 64,973,826 (GRCm39)	T476K	probably damaging	Het
Tlr11	A	T	14: 50,598,691 (GRCm39)	T226S	probably benign	Het
Tmem131	G	A	1: 36,843,680 (GRCm39)	Q1394*	probably null	Het
Tmem161a	C	T	8: 70,629,559 (GRCm39)	R58W	probably damaging	Het
Tmem219	T	C	7: 126,496,422 (GRCm39)	S13G	probably benign	Het
Trp53bp1	T	C	2: 121,035,517 (GRCm39)	Y47C	probably damaging	Het
Ttn	T	A	2: 76,731,922 (GRCm39)		probably benign	Het
Ush1g	A	G	11: 115,209,280 (GRCm39)	S305P	probably damaging	Het
Usp37	A	T	1: 74,479,127 (GRCm39)	Y948*	probably null	Het
Vav1	A	T	17: 57,634,697 (GRCm39)	Y805F	probably damaging	Het
Vmn1r59	A	T	7: 5,457,038 (GRCm39)	Y241N	probably damaging	Het
Vmn2r2	T	A	3: 64,034,121 (GRCm39)	Y467F	probably damaging	Het
Vps35l	A	C	7: 118,374,557 (GRCm39)	R352S	probably damaging	Het
Vps54	C	A	11: 21,242,051 (GRCm39)	L389I	probably damaging	Het
Vwa8	G	T	14: 79,162,694 (GRCm39)		probably benign	Het
Wdr19	G	T	5: 65,398,503 (GRCm39)		probably benign	Het
Wnt2b	A	T	3: 104,861,933 (GRCm39)		probably benign	Het
Xirp2	A	G	2: 67,342,039 (GRCm39)	R1427G	possibly damaging	Het
Ylpm1	T	C	12: 85,087,560 (GRCm39)	S1115P	probably damaging	Het
Zfp946	T	A	17: 22,674,406 (GRCm39)	C387S	probably damaging	Het

Other mutations in Capn3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
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'- TTCAAAAGAAGAGCGCTGGC -3'
(R):5'- TGCCAAAAGACTTCCTTTAGTGTG -3'

Sequencing Primer
(F):5'- GGCTCTCCTCTTGGATGGC -3'
(R):5'- TATAGGCCATGGTATGTGCACAC -3'

Posted On

2014-08-25