Mutagenetix > Incidental Mutation

Incidental Mutation 'R1994:Capn3'

224085

Institutional Source

Beutler Lab

Gene Symbol

Capn3

Ensembl Gene

ENSMUSG00000079110

Gene Name

calpain 3

Synonyms

Capa3, Lp82, Capa-3, p94

Accession Numbers

Essential gene?

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

Stock #

R1994 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

120294074-120335400 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 120326418 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Asparagine at position 537 (Y537N)

Ref Sequence

ENSEMBL: ENSMUSP00000028749 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028748] [ENSMUST00000028749] [ENSMUST00000090028] [ENSMUST00000110716] [ENSMUST00000110719] [ENSMUST00000110721]

AlphaFold

Q64691

Predicted Effect

probably damaging
Transcript: ENSMUST00000028748
AA Change: Y469N

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000028748
Gene: ENSMUSG00000079110
AA Change: Y469N

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

probably damaging
Transcript: ENSMUST00000028749
AA Change: Y537N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000028749
Gene: ENSMUSG00000079110
AA Change: Y537N

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

probably damaging
Transcript: ENSMUST00000090028
AA Change: Y469N

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000087482
Gene: ENSMUSG00000079110
AA Change: Y469N

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

probably damaging
Transcript: ENSMUST00000110716
AA Change: Y517N

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000106344
Gene: ENSMUSG00000079110
AA Change: Y517N

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 damaging
Transcript: ENSMUST00000110719
AA Change: Y517N

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000106347
Gene: ENSMUSG00000079110
AA Change: Y517N

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

probably damaging
Transcript: ENSMUST00000110721
AA Change: Y489N

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000106349
Gene: ENSMUSG00000079110
AA Change: Y489N

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: ENSMUST00000125238

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139336

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145993

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.1%

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: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb11	A	T	2: 69,113,014 (GRCm39)		probably null	Het
Abcc8	T	G	7: 45,806,543 (GRCm39)	R388S	probably benign	Het
Abhd18	C	T	3: 40,889,361 (GRCm39)	R414*	probably null	Het
Acap1	C	T	11: 69,780,324 (GRCm39)	V40I	probably benign	Het
Actn1	C	A	12: 80,251,745 (GRCm39)	G111*	probably null	Het
Adam26b	T	C	8: 43,973,676 (GRCm39)	Q442R	probably benign	Het
Adamts19	T	C	18: 59,105,903 (GRCm39)		probably null	Het
Agtpbp1	T	G	13: 59,678,872 (GRCm39)	K145N	probably damaging	Het
AI661453	A	G	17: 47,777,959 (GRCm39)		probably benign	Het
Ap4e1	T	C	2: 126,903,467 (GRCm39)	S790P	probably benign	Het
Asmt	A	G	X: 169,109,524 (GRCm39)	E168G	possibly damaging	Het
Atp2a3	T	A	11: 72,866,240 (GRCm39)	S287T	probably damaging	Het
AY358078	T	A	14: 52,063,519 (GRCm39)	D388E	probably damaging	Het
Bicd1	A	T	6: 149,415,050 (GRCm39)	T588S	probably benign	Het
Birc6	T	G	17: 74,905,057 (GRCm39)	N1283K	probably benign	Het
Cacna1e	T	A	1: 154,353,563 (GRCm39)	Q423L	probably damaging	Het
Ccn3	T	A	15: 54,612,750 (GRCm39)	V253E	probably benign	Het
Cep295	C	T	9: 15,252,179 (GRCm39)	E397K	probably damaging	Het
Chgb	T	C	2: 132,628,418 (GRCm39)	S48P	possibly damaging	Het
Cidec	T	A	6: 113,405,193 (GRCm39)	Y159F	probably damaging	Het
Clec18a	T	C	8: 111,808,234 (GRCm39)	S66G	possibly damaging	Het
Cpsf1	G	A	15: 76,487,360 (GRCm39)	T138M	probably benign	Het
Dclre1c	C	T	2: 3,439,022 (GRCm39)	R61W	probably damaging	Het
Eef1akmt1	A	C	14: 57,787,911 (GRCm39)	V149G	probably benign	Het
Fam131b	T	C	6: 42,297,818 (GRCm39)	T112A	possibly damaging	Het
Fbln2	A	G	6: 91,211,283 (GRCm39)	E409G	probably damaging	Het
Fkbp15	G	A	4: 62,222,618 (GRCm39)	P1094S	probably benign	Het
Fpr1	A	G	17: 18,097,879 (GRCm39)	S37P	probably benign	Het
Fryl	G	T	5: 73,265,836 (GRCm39)	T495K	probably damaging	Het
Gja6	A	T	X: 159,686,374 (GRCm39)	I186N	possibly damaging	Het
Gm4922	T	C	10: 18,659,388 (GRCm39)	T445A	probably benign	Het
Gria2	G	A	3: 80,709,664 (GRCm39)	L10F	probably benign	Het
Gspt2	A	G	X: 93,681,025 (GRCm39)	D388G	possibly damaging	Het
Hdc	T	A	2: 126,458,107 (GRCm39)	I72F	probably damaging	Het
Ift70b	A	G	2: 75,768,402 (GRCm39)	L117P	probably damaging	Het
Igf2r	T	C	17: 12,911,625 (GRCm39)	K1905E	probably benign	Het
Il33	A	G	19: 29,934,304 (GRCm39)	D155G	possibly damaging	Het
Klk1b9	C	T	7: 43,628,979 (GRCm39)	T161I	probably benign	Het
Mfsd12	C	A	10: 81,193,515 (GRCm39)	H28Q	probably damaging	Het
Mgat5	A	T	1: 127,387,696 (GRCm39)	I551F	possibly damaging	Het
Miga2	A	T	2: 30,272,000 (GRCm39)	D25V	probably damaging	Het
Mlc1	T	C	15: 88,858,782 (GRCm39)	N122S	possibly damaging	Het
Mmp20	T	A	9: 7,645,293 (GRCm39)	M281K	probably benign	Het
Muc5ac	C	A	7: 141,366,889 (GRCm39)	P2232T	possibly damaging	Het
N4bp2l2	A	G	5: 150,584,748 (GRCm39)	S411P	possibly damaging	Het
Ngef	G	A	1: 87,415,626 (GRCm39)	S346L	probably damaging	Het
Or10j27	C	T	1: 172,958,418 (GRCm39)	R122H	possibly damaging	Het
Or2t6	A	G	14: 14,175,854 (GRCm38)	I76T	probably benign	Het
Or4c112	T	A	2: 88,853,487 (GRCm39)	T287S	probably damaging	Het
Or4f15	T	A	2: 111,814,429 (GRCm39)	M5L	probably benign	Het
Or51aa2	T	C	7: 103,187,566 (GRCm39)	I292V	possibly damaging	Het
Or52m2	C	T	7: 102,263,747 (GRCm39)	V150M	probably damaging	Het
Or56b2	T	C	7: 104,337,690 (GRCm39)	I156T	probably benign	Het
Or6c215	T	C	10: 129,637,530 (GRCm39)	Y288C	probably damaging	Het
Or6c6	T	A	10: 129,186,561 (GRCm39)	I43N	probably damaging	Het
Pecam1	G	T	11: 106,586,763 (GRCm39)	H150N	possibly damaging	Het
Polr3c	A	T	3: 96,621,689 (GRCm39)		probably null	Het
Pop1	A	C	15: 34,530,617 (GRCm39)	Q1005P	probably damaging	Het
Prss22	G	A	17: 24,215,288 (GRCm39)	P163S	probably damaging	Het
Prss33	G	A	17: 24,053,172 (GRCm39)	A223V	probably damaging	Het
Prss53	C	T	7: 127,486,565 (GRCm39)	V354I	probably benign	Het
Rab3gap2	C	T	1: 184,968,221 (GRCm39)	T191I	probably damaging	Het
Rictor	T	C	15: 6,805,637 (GRCm39)	F608L	probably benign	Het
Ryr3	T	A	2: 112,484,837 (GRCm39)	E3884V	probably null	Het
Scaf11	G	A	15: 96,316,721 (GRCm39)	R948*	probably null	Het
Sec61g	A	T	11: 16,456,444 (GRCm39)	V40E	probably damaging	Het
Serpinb3d	A	T	1: 107,008,518 (GRCm39)	F116I	possibly damaging	Het
Sipa1l3	T	C	7: 29,099,036 (GRCm39)	D411G	probably benign	Het
Slc13a3	T	C	2: 165,275,984 (GRCm39)	N254S	possibly damaging	Het
Slc35a2	T	A	X: 7,759,064 (GRCm39)	L110Q	probably damaging	Het
Spata31d1b	G	C	13: 59,864,194 (GRCm39)	L447F	probably benign	Het
Spsb2	T	C	6: 124,786,329 (GRCm39)		probably null	Het
Tent4b	C	T	8: 88,973,112 (GRCm39)	T277M	probably damaging	Het
Tmcc3	T	C	10: 94,414,468 (GRCm39)	S57P	possibly damaging	Het
Traf7	A	G	17: 24,729,476 (GRCm39)	V445A	probably damaging	Het
Trib1	A	G	15: 59,521,192 (GRCm39)	S61G	possibly damaging	Het
Trip12	A	T	1: 84,726,893 (GRCm39)	F36I	probably damaging	Het
Tshz3	T	C	7: 36,469,247 (GRCm39)	I412T	probably damaging	Het
Tsku	T	C	7: 98,001,353 (GRCm39)	Y326C	probably damaging	Het
Ttn	T	G	2: 76,712,038 (GRCm39)		probably benign	Het
Ugt1a6a	G	A	1: 88,066,470 (GRCm39)	R92H	probably benign	Het
Vmn1r63	A	G	7: 5,806,254 (GRCm39)	V126A	probably benign	Het
Vmn2r84	T	A	10: 130,221,878 (GRCm39)	S781C	probably damaging	Het
Wdr91	T	A	6: 34,869,297 (GRCm39)	H409L	probably damaging	Het
Wnt7a	T	A	6: 91,342,938 (GRCm39)	T315S	possibly damaging	Het
Zdhhc25	A	G	15: 88,485,027 (GRCm39)	T121A	probably benign	Het
Zfp109	T	C	7: 23,928,743 (GRCm39)	H222R	probably benign	Het
Zfp286	A	G	11: 62,670,646 (GRCm39)	S476P	probably damaging	Het
Zfp605	T	C	5: 110,275,418 (GRCm39)	Y179H	probably damaging	Het
Zfp955a	T	C	17: 33,460,620 (GRCm39)	H504R	probably damaging	Het
Zswim2	T	A	2: 83,746,007 (GRCm39)	N477I	possibly 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
R1971:Capn3	UTSW	2	120,311,228 (GRCm39)	missense	possibly damaging	0.95
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'- TCAGCAATTTGAGGCCTTAGG -3'
(R):5'- AGTGACCTCTTAGCGGTAGGTG -3'

Sequencing Primer
(F):5'- CAATTTGAGGCCTTAGGAACTG -3'
(R):5'- CTCTTAGCGGTAGGTGGGGAAAG -3'

Posted On

2014-08-25