Mutagenetix > Incidental Mutation

Incidental Mutation 'R4796:Capn3'

369019

Institutional Source

Beutler Lab

Gene Symbol

Capn3

Ensembl Gene

ENSMUSG00000079110

Gene Name

calpain 3

Synonyms

Capa-3, Capa3, Lp82, p94

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.383) question?

Stock #

R4796 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

120456019-120504913 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 120502998 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Isoleucine at position 621 (N621I)

Ref Sequence

ENSEMBL: ENSMUSP00000106349 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028748] [ENSMUST00000028749] [ENSMUST00000055241] [ENSMUST00000090028] [ENSMUST00000110716] [ENSMUST00000110719] [ENSMUST00000110721]

AlphaFold

Q64691

Predicted Effect

probably damaging
Transcript: ENSMUST00000028748
AA Change: N601I

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000028748
Gene: ENSMUSG00000079110
AA Change: N601I

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: N713I

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000028749
Gene: ENSMUSG00000079110
AA Change: N713I

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 benign
Transcript: ENSMUST00000055241

SMART Domains

Protein: ENSMUSP00000055602
Gene: ENSMUSG00000027288

Domain	Start	End	E-Value	Type
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

probably damaging
Transcript: ENSMUST00000090028
AA Change: N629I

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000087482
Gene: ENSMUSG00000079110
AA Change: N629I

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: N649I

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000106344
Gene: ENSMUSG00000079110
AA Change: N649I

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: N677I

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000106347
Gene: ENSMUSG00000079110
AA Change: N677I

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: N621I

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000106349
Gene: ENSMUSG00000079110
AA Change: N621I

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: ENSMUST00000141181

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145993

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151342

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.8%

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9230104L09Rik	A	G	2: 148,850,738	F48S	probably damaging	Het
9930021J03Rik	G	A	19: 29,753,618	H665Y	probably benign	Het
Adgrv1	C	T	13: 81,155,231	W132*	probably null	Het
Atp8b3	A	G	10: 80,524,354	V961A	probably damaging	Het
Bglap	A	C	3: 88,384,405	I4S	unknown	Het
Bmp1	T	C	14: 70,492,073		probably null	Het
Btaf1	T	C	19: 36,956,428	L152P	possibly damaging	Het
Cacna1b	T	A	2: 24,637,487	T1621S	possibly damaging	Het
Ccdc59	T	C	10: 105,841,568	S23P	probably benign	Het
Cd22	A	T	7: 30,872,956		probably null	Het
Cdh20	A	G	1: 104,941,264	D160G	probably damaging	Het
Cep112	T	C	11: 108,486,992		probably null	Het
Clock	T	C	5: 76,265,916	K44R	probably damaging	Het
Coq10b	A	G	1: 55,071,798	T242A	probably damaging	Het
Ctnnd1	G	T	2: 84,619,926	R317S	probably damaging	Het
Dlg5	G	A	14: 24,144,383	H1674Y	probably damaging	Het
Drc3	C	A	11: 60,363,528	N75K	probably damaging	Het
Efna4	T	C	3: 89,335,248	E113G	probably damaging	Het
Egr3	C	A	14: 70,077,575	A44D	probably benign	Het
Ercc3	T	C	18: 32,248,310	F393S	probably damaging	Het
Evi2	T	A	11: 79,515,447		probably benign	Het
Fam78b	T	C	1: 167,078,647	V125A	probably benign	Het
Fars2	A	T	13: 36,537,426	E448V	probably damaging	Het
Farsb	A	T	1: 78,425,196	*590R	probably null	Het
Fat3	A	G	9: 15,999,732	M1658T	probably benign	Het
Fhod3	G	T	18: 24,985,301	V232F	probably damaging	Het
Fkbpl	G	A	17: 34,645,329	A24T	probably benign	Het
Fzd3	A	G	14: 65,235,158	V387A	possibly damaging	Het
Gm14085	T	A	2: 122,514,459	I182N	probably damaging	Het
Gm1527	A	G	3: 28,920,663	I542V	possibly damaging	Het
Gm6583	A	G	5: 112,355,299	S180P	possibly damaging	Het
Gm7964	A	G	7: 83,755,901		probably null	Het
Hbs1l	G	T	10: 21,342,506	G301C	probably damaging	Het
Hipk4	A	G	7: 27,528,570	H247R	probably benign	Het
Hmcn1	A	G	1: 150,753,611	V965A	probably benign	Het
Hoxa5	C	T	6: 52,203,963	A130T	probably benign	Het
Igf2r	C	T	17: 12,684,126	V2346I	possibly damaging	Het
Igsf8	T	C	1: 172,316,322	V14A	probably benign	Het
Impg1	G	A	9: 80,394,095	P183L	probably damaging	Het
Isl1	T	C	13: 116,305,430	N89S	probably benign	Het
Itga1	C	A	13: 115,035,385	W61C	probably damaging	Het
Itga5	T	C	15: 103,347,760	R922G	probably benign	Het
Itgb5	T	C	16: 33,885,021	V227A	possibly damaging	Het
Jph4	G	T	14: 55,109,708	P461T	probably damaging	Het
Kcnab1	T	A	3: 65,304,165		probably null	Het
Klrc1	T	A	6: 129,677,762		probably null	Het
Lonrf2	A	T	1: 38,816,038	L92Q	probably benign	Het
Ly75	T	C	2: 60,349,940	E631G	probably benign	Het
Mapk13	T	C	17: 28,775,554	Y140H	probably damaging	Het
Mgat4d	A	G	8: 83,358,120	E164G	probably damaging	Het
Mkl1	C	T	15: 81,017,033	S419N	probably damaging	Het
Mthfs	A	T	9: 89,240,025	H188L	probably benign	Het
Muc5b	T	A	7: 141,864,246	M3643K	possibly damaging	Het
Mylk3	T	C	8: 85,350,385	Y474C	probably damaging	Het
Myo5b	A	G	18: 74,744,630	T1567A	possibly damaging	Het
Ncaph2	T	G	15: 89,370,807	V478G	probably damaging	Het
Ncbp1	A	G	4: 46,152,967	R247G	possibly damaging	Het
Nedd9	T	C	13: 41,317,900	K208E	probably benign	Het
Nxph2	C	T	2: 23,399,858	T74M	probably benign	Het
Ogdh	T	A	11: 6,340,570	M385K	probably benign	Het
Olfr1239	T	C	2: 89,417,891	H174R	probably damaging	Het
Olfr2	C	T	7: 107,001,335	G175D	probably damaging	Het
Olfr402	A	T	11: 74,155,591	I146F	probably benign	Het
Olfr713	A	T	7: 107,036,914	Y253F	probably benign	Het
Olfr830	T	C	9: 18,876,179	V284A	probably damaging	Het
Olfr921	T	A	9: 38,775,374	F40I	probably benign	Het
Pcsk2	A	C	2: 143,813,425	I510L	probably benign	Het
Pdgfra	A	G	5: 75,189,311	N952S	probably benign	Het
Pex26	T	C	6: 121,193,557	F287S	probably damaging	Het
Pick1	G	C	15: 79,255,610		probably benign	Het
Plxnb1	G	T	9: 109,114,595	V1917L	probably damaging	Het
Polk	T	C	13: 96,489,256	T347A	probably benign	Het
Ppp1r10	T	G	17: 35,924,087	I61R	probably damaging	Het
Prex1	A	T	2: 166,592,291	L503Q	probably damaging	Het
Ptp4a1	A	C	1: 30,943,938	I133R	probably damaging	Het
Rassf10	G	T	7: 112,954,528	R112L	probably damaging	Het
Ripor3	T	A	2: 167,981,340	I884F	probably damaging	Het
Rnft2	A	G	5: 118,201,246	Y369H	probably damaging	Het
Rtp3	A	T	9: 110,986,454	V281E	probably benign	Het
Runx1t1	T	A	4: 13,837,767	N51K	probably damaging	Het
Selp	A	G	1: 164,144,906	T705A	probably benign	Het
Sgca	A	T	11: 94,970,727		probably null	Het
Slc22a3	T	C	17: 12,423,788	E514G	probably damaging	Het
Slc2a1	G	A	4: 119,132,445	R61Q	probably damaging	Het
Smarcal1	G	A	1: 72,597,440	V425I	probably benign	Het
Soga1	A	G	2: 157,020,252	S1586P	probably benign	Het
Ssx2ip	T	C	3: 146,418,359	V43A	probably benign	Het
Synpo	A	G	18: 60,604,314	S187P	probably damaging	Het
Thnsl1	T	A	2: 21,212,045	C203*	probably null	Het
Tldc1	A	T	8: 119,768,354	S222T	probably benign	Het
Ttyh3	A	T	5: 140,634,786	I232N	probably damaging	Het
Upk1b	T	C	16: 38,787,242	H41R	probably benign	Het
Vmn2r76	T	C	7: 86,230,444	D216G	possibly damaging	Het
Zan	A	T	5: 137,380,850	C5329*	probably null	Het
Zbtb40	C	T	4: 136,998,642	M535I	probably benign	Het
Zfp383	A	C	7: 29,914,838	T173P	possibly damaging	Het
Zfp7	T	A	15: 76,891,346	C529*	probably null	Het

Other mutations in Capn3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00543:Capn3	APN	2	120486482	intron	probably benign
IGL00976:Capn3	APN	2	120491901	missense	possibly damaging	0.81
IGL01538:Capn3	APN	2	120502186	splice site	probably null
IGL01564:Capn3	APN	2	120480708	missense	probably damaging	1.00
IGL02527:Capn3	APN	2	120504485	missense	probably damaging	0.99
IGL02605:Capn3	APN	2	120496037	missense	probably damaging	0.98
IGL02678:Capn3	APN	2	120502998	missense	probably damaging	1.00
IGL02899:Capn3	APN	2	120491901	missense	possibly damaging	0.81
IGL03255:Capn3	APN	2	120489708	missense	probably damaging	1.00
R0053:Capn3	UTSW	2	120491837	missense	possibly damaging	0.95
R0053:Capn3	UTSW	2	120491837	missense	possibly damaging	0.95
R0096:Capn3	UTSW	2	120502529	missense	possibly damaging	0.94
R0096:Capn3	UTSW	2	120502529	missense	possibly damaging	0.94
R0276:Capn3	UTSW	2	120488065	splice site	probably benign
R0601:Capn3	UTSW	2	120502596	splice site	probably null
R0714:Capn3	UTSW	2	120491880	missense	probably benign	0.32
R1217:Capn3	UTSW	2	120486421	nonsense	probably null
R1530:Capn3	UTSW	2	120482208	missense	probably damaging	1.00
R1566:Capn3	UTSW	2	120502993	missense	possibly damaging	0.72
R1745:Capn3	UTSW	2	120489689	missense	possibly damaging	0.87
R1748:Capn3	UTSW	2	120497013	missense	probably benign	0.10
R1861:Capn3	UTSW	2	120486482	intron	probably benign
R1960:Capn3	UTSW	2	120463940	missense	probably benign	0.00
R1971:Capn3	UTSW	2	120480747	missense	possibly damaging	0.95
R1994:Capn3	UTSW	2	120495937	missense	probably damaging	1.00
R2043:Capn3	UTSW	2	120491901	missense	possibly damaging	0.81
R2254:Capn3	UTSW	2	120501251	missense	probably benign	0.01
R2255:Capn3	UTSW	2	120501251	missense	probably benign	0.01
R3738:Capn3	UTSW	2	120485287	missense	possibly damaging	0.85
R3824:Capn3	UTSW	2	120484483	splice site	probably benign
R5073:Capn3	UTSW	2	120491820	missense	probably damaging	1.00
R5116:Capn3	UTSW	2	120485292	missense	probably benign	0.00
R5152:Capn3	UTSW	2	120501330	intron	probably benign
R5420:Capn3	UTSW	2	120495296	intron	probably benign
R5478:Capn3	UTSW	2	120464185	splice site	probably null
R5506:Capn3	UTSW	2	120502420	missense	probably damaging	0.97
R5664:Capn3	UTSW	2	120477025	missense	probably benign	0.04
R5733:Capn3	UTSW	2	120484594	nonsense	probably null
R6212:Capn3	UTSW	2	120477186	missense	probably benign	0.17
R7176:Capn3	UTSW	2	120504492	missense	possibly damaging	0.46
R7219:Capn3	UTSW	2	120503454	missense	probably damaging	0.99
R7365:Capn3	UTSW	2	120494814	missense	probably damaging	0.98
R7819:Capn3	UTSW	2	120464165	missense	probably benign	0.05
R8052:Capn3	UTSW	2	120486386	missense	probably benign
R8834:Capn3	UTSW	2	120464053	missense	probably damaging	0.98
R8970:Capn3	UTSW	2	120464085	missense	possibly damaging	0.90
R9088:Capn3	UTSW	2	120490970	missense	probably benign
R9473:Capn3	UTSW	2	120496054	nonsense	probably null
R9512:Capn3	UTSW	2	120496054	missense	probably damaging	0.99
R9663:Capn3	UTSW	2	120486378	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- GCTGTAAAGCTGGCAGGAAC -3'
(R):5'- TGCATCATTGACTGCATTTCGC -3'

Sequencing Primer
(F):5'- CTGGCAGGAACTCTGGTTAAG -3'
(R):5'- CATCTCATAGCTATTGATGGTACCGG -3'

Posted On

2016-02-04