Mutagenetix > Incidental Mutation

Incidental Mutation 'R7365:Capn3'

571681

Institutional Source

Beutler Lab

Gene Symbol

Capn3

Ensembl Gene

ENSMUSG00000079110

Gene Name

calpain 3

Synonyms

Capa3, Lp82, Capa-3, p94

MMRRC Submission

045449-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.217) question?

Stock #

R7365 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

120294074-120335400 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 120325295 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 466 (E466G)

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: E398G

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000028748
Gene: ENSMUSG00000079110
AA Change: E398G

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: E466G

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

SMART Domains

Protein: ENSMUSP00000028749
Gene: ENSMUSG00000079110
AA Change: E466G

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: E398G

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

SMART Domains

Protein: ENSMUSP00000087482
Gene: ENSMUSG00000079110
AA Change: E398G

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: E446G

PolyPhen 2 Score 0.912 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000106344
Gene: ENSMUSG00000079110
AA Change: E446G

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: E446G

PolyPhen 2 Score 0.327 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000106347
Gene: ENSMUSG00000079110
AA Change: E446G

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: E418G

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000106349
Gene: ENSMUSG00000079110
AA Change: E418G

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

Meta Mutation Damage Score

0.3097

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

100% (96/96)

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: 96 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700123K08Rik	T	C	5: 138,561,198 (GRCm39)	S155G	probably benign	Het
Abcc4	T	C	14: 118,865,066 (GRCm39)	N320S	probably damaging	Het
Akr1c19	G	A	13: 4,287,069 (GRCm39)	R96H	probably benign	Het
Ankrd17	T	C	5: 90,439,010 (GRCm39)	D451G	possibly damaging	Het
Ano8	T	A	8: 71,937,754 (GRCm39)	D36V	probably damaging	Het
Aqp3	A	G	4: 41,098,003 (GRCm39)	V36A	probably benign	Het
Atf7ip	A	G	6: 136,537,708 (GRCm39)	T314A	probably benign	Het
Atp2c1	A	T	9: 105,300,198 (GRCm39)	D700E	probably damaging	Het
Axin2	G	A	11: 108,830,202 (GRCm39)	V341M	possibly damaging	Het
Bin3	A	G	14: 70,371,976 (GRCm39)	Q139R	probably damaging	Het
Brca2	A	G	5: 150,455,802 (GRCm39)	D181G	probably damaging	Het
Ccdc14	T	A	16: 34,543,989 (GRCm39)	Y830*	probably null	Het
Cdk12	T	C	11: 98,111,910 (GRCm39)	F723L	unknown	Het
Cep89	G	A	7: 35,129,353 (GRCm39)	R630H	probably damaging	Het
Cip2a	T	A	16: 48,822,016 (GRCm39)	S215T	probably benign	Het
Clca3a2	T	A	3: 144,804,545 (GRCm39)	I61F	probably damaging	Het
Clca4b	T	C	3: 144,628,529 (GRCm39)	T393A	not run	Het
Cldn5	G	A	16: 18,595,845 (GRCm39)	A34T	probably damaging	Het
Cobll1	A	T	2: 64,928,717 (GRCm39)	S870T	probably damaging	Het
Col12a1	T	C	9: 79,613,642 (GRCm39)	K68E	probably damaging	Het
Crnn	A	T	3: 93,055,841 (GRCm39)	Q209L	probably damaging	Het
Cwf19l1	A	T	19: 44,120,579 (GRCm39)	F45I	probably damaging	Het
Cyfip2	T	A	11: 46,098,267 (GRCm39)	K1052*	probably null	Het
D930020B18Rik	G	A	10: 121,503,716 (GRCm39)		probably null	Het
Dcc	G	A	18: 71,959,194 (GRCm39)	P193S	probably damaging	Het
Dda1	T	A	8: 71,927,137 (GRCm39)	C48S	probably benign	Het
Disc1	A	G	8: 125,881,780 (GRCm39)	R572G	probably damaging	Het
Dnah7a	A	T	1: 53,536,297 (GRCm39)	M2582K	probably benign	Het
Dsel	C	T	1: 111,789,303 (GRCm39)	G411S	probably damaging	Het
Dynlrb2	T	C	8: 117,241,696 (GRCm39)	V80A	probably benign	Het
Eif3a	A	T	19: 60,755,082 (GRCm39)	D1033E	unknown	Het
Enam	C	A	5: 88,649,347 (GRCm39)	H285Q	possibly damaging	Het
Ep400	T	C	5: 110,867,480 (GRCm39)	D980G	unknown	Het
Epha7	C	T	4: 28,871,937 (GRCm39)	S422L	probably benign	Het
Erc2	A	C	14: 27,762,346 (GRCm39)	D703A	probably damaging	Het
Ezh2	G	T	6: 47,510,692 (GRCm39)	S639*	probably null	Het
Fbn1	G	A	2: 125,193,969 (GRCm39)	H1333Y	probably damaging	Het
Flad1	A	G	3: 89,315,972 (GRCm39)	S197P	possibly damaging	Het
Foxl3	A	G	5: 138,806,736 (GRCm39)	H82R	probably damaging	Het
Gfm2	G	T	13: 97,279,529 (GRCm39)	C26F	probably benign	Het
Golga2	C	T	2: 32,193,013 (GRCm39)	Q444*	probably null	Het
Gp5	A	T	16: 30,127,426 (GRCm39)	V416D	probably damaging	Het
Gpat2	A	G	2: 127,268,901 (GRCm39)		probably null	Het
Gpr137c	A	G	14: 45,516,471 (GRCm39)	D353G	probably damaging	Het
Hoxa13	A	C	6: 52,236,862 (GRCm39)	W133G	probably damaging	Het
Hydin	A	T	8: 111,284,294 (GRCm39)	I3189F	probably damaging	Het
Hydin	A	T	8: 111,327,905 (GRCm39)	K4804M	probably damaging	Het
Ice2	T	C	9: 69,307,794 (GRCm39)	F26S	probably damaging	Het
Ints11	T	C	4: 155,956,687 (GRCm39)		probably null	Het
Ipo5	A	G	14: 121,157,497 (GRCm39)	I112V	probably benign	Het
Itgax	T	A	7: 127,734,481 (GRCm39)	S346R	probably damaging	Het
Kcnj13	T	A	1: 87,316,739 (GRCm39)	M125L	probably damaging	Het
Lmbrd1	T	A	1: 24,783,948 (GRCm39)	V359E	possibly damaging	Het
Lrrc7	T	G	3: 157,903,798 (GRCm39)	K287N	probably damaging	Het
Mau2	C	T	8: 70,481,884 (GRCm39)	A191T	possibly damaging	Het
Mkx	C	A	18: 7,000,747 (GRCm39)	R65L	possibly damaging	Het
Mroh4	T	A	15: 74,482,220 (GRCm39)	K746*	probably null	Het
Myh4	A	G	11: 67,133,674 (GRCm39)	T238A	probably damaging	Het
Nlrp9c	T	A	7: 26,070,822 (GRCm39)	N920Y	possibly damaging	Het
Nr4a3	T	G	4: 48,051,290 (GRCm39)	S15A	possibly damaging	Het
Ntn4	T	C	10: 93,480,666 (GRCm39)	L130P	probably damaging	Het
Or2ag13	A	G	7: 106,313,171 (GRCm39)	V239A	probably benign	Het
Or4a68	A	G	2: 89,270,542 (GRCm39)	V27A	probably benign	Het
Or4f59	A	T	2: 111,873,359 (GRCm39)	V6E	possibly damaging	Het
Or56a42-ps1	T	A	7: 104,777,552 (GRCm39)	I21F	probably benign	Het
Or8d23	A	T	9: 38,842,072 (GRCm39)	I202F	probably damaging	Het
Otog	T	C	7: 45,947,732 (GRCm39)	L110P	probably damaging	Het
Platr25	G	A	13: 62,848,719 (GRCm39)	H48Y	probably benign	Het
Plcxd2	T	C	16: 45,800,789 (GRCm39)	E145G	probably damaging	Het
Pltp	A	T	2: 164,696,242 (GRCm39)	N143K	probably damaging	Het
Pnpt1	T	C	11: 29,111,334 (GRCm39)	Y735H	probably damaging	Het
Prom1	A	G	5: 44,178,173 (GRCm39)	Y520H	probably damaging	Het
Rag2	A	G	2: 101,461,118 (GRCm39)	Y476C	probably damaging	Het
Rdh16f2	A	G	10: 127,712,893 (GRCm39)	Y297C	probably damaging	Het
Ryr1	T	C	7: 28,785,180 (GRCm39)	E1844G	probably benign	Het
Ryr2	A	G	13: 11,655,161 (GRCm39)	C3679R	probably damaging	Het
Sirt1	A	G	10: 63,157,782 (GRCm39)	I544T	probably benign	Het
Slc26a10	A	T	10: 127,012,716 (GRCm39)	I382N	possibly damaging	Het
Sox2	C	A	3: 34,705,121 (GRCm39)	P186Q	possibly damaging	Het
Spata31e5	A	T	1: 28,819,233 (GRCm39)	M16K	probably benign	Het
Tnpo3	A	G	6: 29,556,995 (GRCm39)	L752P	probably damaging	Het
Top2b	T	A	14: 16,416,649 (GRCm38)	N1136K	probably benign	Het
Tpsg1	G	T	17: 25,592,184 (GRCm39)	G86V	probably damaging	Het
Ttf2	C	A	3: 100,870,618 (GRCm39)	D152Y	possibly damaging	Het
Txndc15	T	C	13: 55,862,601 (GRCm39)	L4P	unknown	Het
Unc5a	T	C	13: 55,144,386 (GRCm39)	V237A	possibly damaging	Het
Urb1	CACTTAC	CAC	16: 90,569,461 (GRCm39)		probably benign	Het
Vav3	C	A	3: 109,535,415 (GRCm39)	P616T	possibly damaging	Het
Vmn2r15	T	A	5: 109,441,105 (GRCm39)	D251V	probably benign	Het
Vmn2r15	A	G	5: 109,445,388 (GRCm39)	L12S	probably benign	Het
Wfs1	A	C	5: 37,125,076 (GRCm39)	I605S	probably benign	Het
Wif1	G	A	10: 120,919,814 (GRCm39)	R187Q	possibly damaging	Het
Yipf1	A	G	4: 107,207,738 (GRCm39)		probably null	Het
Zdhhc20	G	T	14: 58,111,377 (GRCm39)	F74L	possibly damaging	Het
Zfp507	T	C	7: 35,475,843 (GRCm39)	T303A	unknown	Het
Zfp763	A	T	17: 33,252,352 (GRCm39)		probably benign	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
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
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'- ATGCATGCGGTACACAGACATAG -3'
(R):5'- GTTGGAAACTCCCAAGTTCTCC -3'

Sequencing Primer
(F):5'- GCGGTACACAGACATAGGCAAAC -3'
(R):5'- AAGTTCTCCCCGCTGGAAAG -3'

Posted On

2019-09-13