Mutagenetix > Incidental Mutation

Incidental Mutation 'R0403:Smarcc1'

35711

Institutional Source

Beutler Lab

Gene Symbol

Smarcc1

Ensembl Gene

ENSMUSG00000032481

Gene Name

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1

Synonyms

BAF155, SRG3, msp3

MMRRC Submission

038608-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0403 (G1)

Quality Score

195

Status

Validated

Chromosome

Chromosomal Location

109961129-110069773 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to A at 110066876 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000143550 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000088716] [ENSMUST00000088716] [ENSMUST00000088716] [ENSMUST00000197984] [ENSMUST00000199896] [ENSMUST00000199896] [ENSMUST00000199896]

AlphaFold

P97496

Predicted Effect

probably null
Transcript: ENSMUST00000088716

SMART Domains

Protein: ENSMUSP00000086094
Gene: ENSMUSG00000032481

Domain	Start	End	E-Value	Type
low complexity region	2	28	N/A	INTRINSIC
CHROMO	214	260	3.06e-3	SMART
low complexity region	321	333	N/A	INTRINSIC
Pfam:SWIRM	450	536	1.7e-33	PFAM
SANT	618	666	4.52e-12	SMART
Pfam:SWIRM-assoc_3	705	771	9.6e-35	PFAM
low complexity region	830	839	N/A	INTRINSIC
Pfam:SWIRM-assoc_1	870	953	2.5e-34	PFAM
low complexity region	955	973	N/A	INTRINSIC
low complexity region	986	1031	N/A	INTRINSIC
low complexity region	1043	1058	N/A	INTRINSIC
low complexity region	1075	1104	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000088716

SMART Domains

Protein: ENSMUSP00000086094
Gene: ENSMUSG00000032481

Domain	Start	End	E-Value	Type
low complexity region	2	28	N/A	INTRINSIC
CHROMO	214	260	3.06e-3	SMART
low complexity region	321	333	N/A	INTRINSIC
Pfam:SWIRM	450	536	1.7e-33	PFAM
SANT	618	666	4.52e-12	SMART
Pfam:SWIRM-assoc_3	705	771	9.6e-35	PFAM
low complexity region	830	839	N/A	INTRINSIC
Pfam:SWIRM-assoc_1	870	953	2.5e-34	PFAM
low complexity region	955	973	N/A	INTRINSIC
low complexity region	986	1031	N/A	INTRINSIC
low complexity region	1043	1058	N/A	INTRINSIC
low complexity region	1075	1104	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000088716

SMART Domains

Protein: ENSMUSP00000086094
Gene: ENSMUSG00000032481

Domain	Start	End	E-Value	Type
low complexity region	2	28	N/A	INTRINSIC
CHROMO	214	260	3.06e-3	SMART
low complexity region	321	333	N/A	INTRINSIC
Pfam:SWIRM	450	536	1.7e-33	PFAM
SANT	618	666	4.52e-12	SMART
Pfam:SWIRM-assoc_3	705	771	9.6e-35	PFAM
low complexity region	830	839	N/A	INTRINSIC
Pfam:SWIRM-assoc_1	870	953	2.5e-34	PFAM
low complexity region	955	973	N/A	INTRINSIC
low complexity region	986	1031	N/A	INTRINSIC
low complexity region	1043	1058	N/A	INTRINSIC
low complexity region	1075	1104	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000197984

SMART Domains

Protein: ENSMUSP00000142611
Gene: ENSMUSG00000032481

Domain	Start	End	E-Value	Type
low complexity region	2	28	N/A	INTRINSIC
CHROMO	214	260	3.06e-3	SMART
low complexity region	321	333	N/A	INTRINSIC
Pfam:SWIRM	448	536	1.4e-35	PFAM
SANT	618	666	4.52e-12	SMART
low complexity region	710	717	N/A	INTRINSIC
low complexity region	723	734	N/A	INTRINSIC
low complexity region	768	781	N/A	INTRINSIC
low complexity region	830	839	N/A	INTRINSIC
low complexity region	866	885	N/A	INTRINSIC
coiled coil region	909	945	N/A	INTRINSIC
low complexity region	955	973	N/A	INTRINSIC
low complexity region	986	1031	N/A	INTRINSIC
low complexity region	1043	1058	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000198211

Predicted Effect

probably null
Transcript: ENSMUST00000199896

SMART Domains

Protein: ENSMUSP00000143550
Gene: ENSMUSG00000032481

Domain	Start	End	E-Value	Type
low complexity region	2	28	N/A	INTRINSIC
CHROMO	214	260	3.06e-3	SMART
low complexity region	321	333	N/A	INTRINSIC
Pfam:SWIRM	450	536	1.5e-33	PFAM
SANT	618	666	4.52e-12	SMART
Pfam:SWIRM-assoc_3	705	771	1.4e-34	PFAM
low complexity region	830	839	N/A	INTRINSIC
Pfam:SWIRM-assoc_1	870	953	1.4e-34	PFAM
low complexity region	955	973	N/A	INTRINSIC
low complexity region	986	1031	N/A	INTRINSIC
low complexity region	1043	1058	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000199896

SMART Domains

Protein: ENSMUSP00000143550
Gene: ENSMUSG00000032481

Domain	Start	End	E-Value	Type
low complexity region	2	28	N/A	INTRINSIC
CHROMO	214	260	3.06e-3	SMART
low complexity region	321	333	N/A	INTRINSIC
Pfam:SWIRM	450	536	1.5e-33	PFAM
SANT	618	666	4.52e-12	SMART
Pfam:SWIRM-assoc_3	705	771	1.4e-34	PFAM
low complexity region	830	839	N/A	INTRINSIC
Pfam:SWIRM-assoc_1	870	953	1.4e-34	PFAM
low complexity region	955	973	N/A	INTRINSIC
low complexity region	986	1031	N/A	INTRINSIC
low complexity region	1043	1058	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000199896

SMART Domains

Protein: ENSMUSP00000143550
Gene: ENSMUSG00000032481

Domain	Start	End	E-Value	Type
low complexity region	2	28	N/A	INTRINSIC
CHROMO	214	260	3.06e-3	SMART
low complexity region	321	333	N/A	INTRINSIC
Pfam:SWIRM	450	536	1.5e-33	PFAM
SANT	618	666	4.52e-12	SMART
Pfam:SWIRM-assoc_3	705	771	1.4e-34	PFAM
low complexity region	830	839	N/A	INTRINSIC
Pfam:SWIRM-assoc_1	870	953	1.4e-34	PFAM
low complexity region	955	973	N/A	INTRINSIC
low complexity region	986	1031	N/A	INTRINSIC
low complexity region	1043	1058	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000200426

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 98.0%
3x: 96.8%
10x: 93.2%
20x: 83.7%

Validation Efficiency

97% (110/113)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI and contains a predicted leucine zipper motif typical of many transcription factors. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out mutation display early embryonic lethality soon after decidualization due to failed egg cylinder formation and defects in the inner cell mass and primitive endoderm. About 20% of heterozygous mutant embryos show exencephaly caused by failure in neural fold elevation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ace	A	G	11: 105,864,706 (GRCm39)		probably null	Het
Adgrg3	C	T	8: 95,763,550 (GRCm39)	L284F	probably benign	Het
Alkbh8	T	A	9: 3,385,469 (GRCm39)	V587E	probably damaging	Het
Ap4b1	T	A	3: 103,728,712 (GRCm39)	M590K	probably benign	Het
Ap4b1	T	A	3: 103,726,155 (GRCm39)	C244S	probably damaging	Het
Arhgap15	C	T	2: 43,953,778 (GRCm39)	T168I	probably damaging	Het
Atp8b1	A	G	18: 64,673,381 (GRCm39)	V997A	probably damaging	Het
Atrn	G	A	2: 130,748,779 (GRCm39)	C100Y	probably damaging	Het
Baiap2l2	C	A	15: 79,155,416 (GRCm39)	A151S	probably benign	Het
Baz2b	A	T	2: 59,799,721 (GRCm39)	D199E	possibly damaging	Het
Bmal2	T	A	6: 146,724,153 (GRCm39)	H348Q	probably damaging	Het
Cblb	A	G	16: 51,972,989 (GRCm39)	D440G	probably benign	Het
Cdon	T	C	9: 35,384,796 (GRCm39)	V694A	probably benign	Het
Cep250	A	T	2: 155,834,269 (GRCm39)	R2065W	probably damaging	Het
Ces2b	G	T	8: 105,560,577 (GRCm39)	A131S	probably damaging	Het
Chrna9	A	T	5: 66,125,235 (GRCm39)	T59S	possibly damaging	Het
Cog3	T	A	14: 75,979,767 (GRCm39)		probably benign	Het
Cpa1	G	A	6: 30,641,856 (GRCm39)	V227I	probably benign	Het
Cyp3a25	A	T	5: 145,935,323 (GRCm39)	C98S	probably damaging	Het
D8Ertd738e	C	T	8: 84,976,230 (GRCm39)		probably null	Het
Ddx60	A	G	8: 62,447,575 (GRCm39)		probably benign	Het
Dhx16	T	C	17: 36,193,942 (GRCm39)		probably null	Het
Dnah9	T	A	11: 65,975,615 (GRCm39)	Q1478L	possibly damaging	Het
Dock10	T	C	1: 80,501,787 (GRCm39)	Y1434C	possibly damaging	Het
Enpp3	T	A	10: 24,680,334 (GRCm39)	D325V	probably damaging	Het
Entpd6	C	A	2: 150,602,090 (GRCm39)	T194K	possibly damaging	Het
Fat2	A	T	11: 55,161,175 (GRCm39)	V3185E	probably benign	Het
Flrt1	A	G	19: 7,073,284 (GRCm39)	L421P	probably benign	Het
Fmn2	A	T	1: 174,521,844 (GRCm39)	Q1292L	probably damaging	Het
Fndc1	T	C	17: 7,972,555 (GRCm39)	D1459G	probably damaging	Het
Fndc1	T	C	17: 7,994,420 (GRCm39)		probably null	Het
Fzr1	A	G	10: 81,205,202 (GRCm39)	S265P	possibly damaging	Het
Gpr142	G	A	11: 114,696,855 (GRCm39)	V134M	probably damaging	Het
Grid2ip	G	T	5: 143,343,375 (GRCm39)	V24L	possibly damaging	Het
Herc2	G	A	7: 55,809,165 (GRCm39)	R2555H	probably damaging	Het
Hpdl	A	T	4: 116,677,676 (GRCm39)	Y262N	possibly damaging	Het
Htr3a	A	G	9: 48,819,959 (GRCm39)	V57A	probably damaging	Het
Igfbp7	T	C	5: 77,503,438 (GRCm39)	I186V	probably benign	Het
Itga2b	C	T	11: 102,358,152 (GRCm39)		probably null	Het
Itgae	A	C	11: 73,014,009 (GRCm39)	D736A	possibly damaging	Het
Itpkc	T	A	7: 26,907,770 (GRCm39)	M645L	probably benign	Het
Jchain	T	C	5: 88,669,237 (GRCm39)	R139G	probably benign	Het
Kif13a	A	G	13: 46,944,877 (GRCm39)	V908A	probably damaging	Het
Kif1b	T	A	4: 149,266,424 (GRCm39)	K389*	probably null	Het
Klhl12	T	C	1: 134,413,594 (GRCm39)	Y360H	possibly damaging	Het
Knop1	G	A	7: 118,452,276 (GRCm39)	R148W	probably damaging	Het
Lpar1	T	A	4: 58,487,191 (GRCm39)	N27Y	probably damaging	Het
Lpar2	T	A	8: 70,276,802 (GRCm39)	V197D	probably damaging	Het
Lrrc74a	A	G	12: 86,787,753 (GRCm39)	N128S	probably damaging	Het
Lum	G	T	10: 97,407,905 (GRCm39)	V337F	probably benign	Het
Mag	T	C	7: 30,606,405 (GRCm39)	D344G	probably damaging	Het
Maip1	G	A	1: 57,446,355 (GRCm39)	A142T	probably benign	Het
Mlh3	A	G	12: 85,315,742 (GRCm39)	V148A	possibly damaging	Het
Nav3	A	G	10: 109,602,964 (GRCm39)	V1195A	probably damaging	Het
Ncor2	A	G	5: 125,110,401 (GRCm39)	S868P	possibly damaging	Het
Nek1	A	G	8: 61,559,889 (GRCm39)	E907G	probably damaging	Het
Nfam1	G	A	15: 82,900,580 (GRCm39)	T134I	probably benign	Het
Nr0b2	T	C	4: 133,281,070 (GRCm39)	V112A	probably damaging	Het
Nrp1	A	G	8: 129,184,450 (GRCm39)	N365S	probably damaging	Het
Nrsn2	T	C	2: 152,211,710 (GRCm39)	Y107C	probably damaging	Het
Ntng1	G	A	3: 109,841,927 (GRCm39)	A282V	probably damaging	Het
Nxf1	T	C	19: 8,742,392 (GRCm39)	I337T	probably damaging	Het
Obscn	C	T	11: 58,967,366 (GRCm39)	G479D	probably damaging	Het
Oprd1	T	A	4: 131,841,079 (GRCm39)	D293V	probably benign	Het
Or13a17	T	C	7: 140,271,222 (GRCm39)	S135P	possibly damaging	Het
P3h2	T	G	16: 25,788,700 (GRCm39)	N586H	possibly damaging	Het
Pcid2	T	C	8: 13,135,367 (GRCm39)	Y214C	probably damaging	Het
Pkd1l3	C	G	8: 110,350,281 (GRCm39)	D375E	possibly damaging	Het
Pkd1l3	G	A	8: 110,350,295 (GRCm39)	S380N	probably benign	Het
Ppic	C	A	18: 53,544,143 (GRCm39)	G81W	probably damaging	Het
Ppp2r1a	C	A	17: 21,177,303 (GRCm39)	P246T	probably damaging	Het
Ppp4r4	T	G	12: 103,550,361 (GRCm39)	S46A	probably benign	Het
Pramel31	A	G	4: 144,089,216 (GRCm39)	N178S	probably benign	Het
Prkce	A	G	17: 86,476,081 (GRCm39)	T21A	probably damaging	Het
Prkg2	T	C	5: 99,142,504 (GRCm39)	E210G	possibly damaging	Het
Prss35	A	G	9: 86,638,090 (GRCm39)	M287V	probably damaging	Het
Psd	G	A	19: 46,309,411 (GRCm39)		probably benign	Het
Ptch2	A	T	4: 116,968,036 (GRCm39)	K843*	probably null	Het
Rab44	C	A	17: 29,364,235 (GRCm39)	T603K	probably damaging	Het
Rasal3	T	A	17: 32,611,764 (GRCm39)		probably null	Het
Rbbp6	A	G	7: 122,591,519 (GRCm39)	T526A	probably damaging	Het
Ros1	A	T	10: 52,019,534 (GRCm39)		probably benign	Het
Sec24b	T	A	3: 129,783,325 (GRCm39)	L1104F	possibly damaging	Het
Sec24b	A	G	3: 129,793,183 (GRCm39)	S685P	probably damaging	Het
Sema6a	G	A	18: 47,423,112 (GRCm39)		probably null	Het
Setmar	A	T	6: 108,052,923 (GRCm39)	H139L	probably benign	Het
Slc28a2b	T	C	2: 122,352,335 (GRCm39)	L364S	probably damaging	Het
Slc4a7	T	C	14: 14,766,808 (GRCm38)	V710A	probably benign	Het
Smchd1	G	A	17: 71,701,897 (GRCm39)	L1032F	probably damaging	Het
Speg	T	C	1: 75,407,428 (GRCm39)		probably benign	Het
Tasor2	A	T	13: 3,632,052 (GRCm39)	Y816*	probably null	Het
Tcea1	C	G	1: 4,959,726 (GRCm39)	R134G	probably benign	Het
Tchhl1	C	T	3: 93,378,336 (GRCm39)	Q347*	probably null	Het
Tecrl	A	T	5: 83,502,605 (GRCm39)		probably benign	Het
Tepsin	T	C	11: 119,984,508 (GRCm39)		probably benign	Het
Tmem40	G	A	6: 115,710,946 (GRCm39)		probably benign	Het
Tpr	G	A	1: 150,283,165 (GRCm39)		probably benign	Het
Ttll12	A	T	15: 83,464,859 (GRCm39)		probably benign	Het
Ttn	T	A	2: 76,739,952 (GRCm39)	D3529V	probably benign	Het
Usp34	T	A	11: 23,283,838 (GRCm39)	H177Q	possibly damaging	Het
Vsig10	T	A	5: 117,476,526 (GRCm39)	S327T	probably benign	Het
Zbtb4	T	A	11: 69,668,465 (GRCm39)	M396K	probably damaging	Het
Zfp352	C	T	4: 90,113,246 (GRCm39)	T462I	possibly damaging	Het
Zfp385b	T	C	2: 77,307,189 (GRCm39)	M145V	probably damaging	Het
Zfp780b	C	A	7: 27,671,114 (GRCm39)	V65F	possibly damaging	Het

Other mutations in Smarcc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01107:Smarcc1	APN	9	110,051,005 (GRCm39)	missense	probably damaging	1.00
IGL01152:Smarcc1	APN	9	109,968,693 (GRCm39)	missense	possibly damaging	0.89
IGL01353:Smarcc1	APN	9	109,964,734 (GRCm39)	missense	probably benign	0.07
IGL01401:Smarcc1	APN	9	109,979,033 (GRCm39)	missense	possibly damaging	0.52
IGL01483:Smarcc1	APN	9	110,051,128 (GRCm39)	nonsense	probably null
IGL01679:Smarcc1	APN	9	110,042,598 (GRCm39)	missense	probably damaging	1.00
IGL02458:Smarcc1	APN	9	109,961,194 (GRCm39)	intron	probably benign
IGL02498:Smarcc1	APN	9	110,020,002 (GRCm39)	missense	probably damaging	1.00
IGL02605:Smarcc1	APN	9	110,051,068 (GRCm39)	missense	possibly damaging	0.86
IGL03003:Smarcc1	APN	9	110,035,168 (GRCm39)	missense	probably damaging	0.97
IGL03284:Smarcc1	APN	9	110,004,142 (GRCm39)	missense	probably benign	0.30
R0116:Smarcc1	UTSW	9	109,976,172 (GRCm39)	missense	possibly damaging	0.71
R1436:Smarcc1	UTSW	9	109,947,708 (GRCm39)	unclassified	probably benign
R1583:Smarcc1	UTSW	9	110,042,685 (GRCm39)	missense	probably damaging	1.00
R1692:Smarcc1	UTSW	9	110,003,072 (GRCm39)	missense	possibly damaging	0.85
R1732:Smarcc1	UTSW	9	110,014,888 (GRCm39)	splice site	probably benign
R1833:Smarcc1	UTSW	9	109,982,879 (GRCm39)	missense	possibly damaging	0.71
R1881:Smarcc1	UTSW	9	110,004,167 (GRCm39)	missense	probably damaging	1.00
R2058:Smarcc1	UTSW	9	109,947,411 (GRCm39)	unclassified	probably benign
R2175:Smarcc1	UTSW	9	109,993,877 (GRCm39)	missense	possibly damaging	0.71
R2215:Smarcc1	UTSW	9	110,066,907 (GRCm39)	utr 3 prime	probably benign
R2904:Smarcc1	UTSW	9	110,003,043 (GRCm39)	missense	possibly damaging	0.80
R3899:Smarcc1	UTSW	9	109,947,586 (GRCm39)	unclassified	probably benign
R3900:Smarcc1	UTSW	9	109,947,586 (GRCm39)	unclassified	probably benign
R4012:Smarcc1	UTSW	9	109,961,273 (GRCm39)	missense	possibly damaging	0.96
R4091:Smarcc1	UTSW	9	109,993,897 (GRCm39)	missense	possibly damaging	0.84
R4356:Smarcc1	UTSW	9	110,025,324 (GRCm39)	missense	probably damaging	0.99
R4881:Smarcc1	UTSW	9	109,964,696 (GRCm39)	start gained	probably benign
R4993:Smarcc1	UTSW	9	110,004,129 (GRCm39)	missense	probably damaging	1.00
R5110:Smarcc1	UTSW	9	110,026,852 (GRCm39)	missense	possibly damaging	0.89
R5375:Smarcc1	UTSW	9	110,020,017 (GRCm39)	missense	probably damaging	0.99
R5655:Smarcc1	UTSW	9	109,986,412 (GRCm39)	missense	probably null	1.00
R5715:Smarcc1	UTSW	9	110,025,435 (GRCm39)	missense	possibly damaging	0.95
R5767:Smarcc1	UTSW	9	109,961,251 (GRCm39)	intron	probably benign
R5816:Smarcc1	UTSW	9	110,026,712 (GRCm39)	missense	possibly damaging	0.51
R6969:Smarcc1	UTSW	9	110,025,388 (GRCm39)	missense	probably damaging	1.00
R7068:Smarcc1	UTSW	9	110,014,952 (GRCm39)	missense	probably damaging	1.00
R7211:Smarcc1	UTSW	9	109,979,082 (GRCm39)	missense	probably damaging	0.97
R7558:Smarcc1	UTSW	9	109,976,184 (GRCm39)	missense	probably damaging	0.96
R7903:Smarcc1	UTSW	9	110,033,334 (GRCm39)	missense	probably benign	0.01
R8190:Smarcc1	UTSW	9	110,031,602 (GRCm39)	missense	probably benign
R8695:Smarcc1	UTSW	9	110,002,972 (GRCm39)	missense	probably damaging	0.98
R8842:Smarcc1	UTSW	9	110,051,199 (GRCm39)	missense	possibly damaging	0.60
R9024:Smarcc1	UTSW	9	110,015,001 (GRCm39)	missense	probably damaging	0.99
R9131:Smarcc1	UTSW	9	109,964,710 (GRCm39)	missense	possibly damaging	0.73
R9180:Smarcc1	UTSW	9	109,964,728 (GRCm39)	missense	probably damaging	1.00
R9279:Smarcc1	UTSW	9	109,996,792 (GRCm39)	missense	possibly damaging	0.69
R9352:Smarcc1	UTSW	9	110,035,220 (GRCm39)	missense	probably null	1.00
R9538:Smarcc1	UTSW	9	109,961,272 (GRCm39)	missense	probably benign	0.00
R9645:Smarcc1	UTSW	9	109,986,410 (GRCm39)	missense	probably damaging	1.00
T0722:Smarcc1	UTSW	9	110,035,153 (GRCm39)	missense	possibly damaging	0.86

Predicted Primers

PCR Primer
(F):5'- TGAGCAACTTCAGCAGCAGTCG -3'
(R):5'- ACAGGCTTCCCAATGAGTGTCAAC -3'

Sequencing Primer
(F):5'- gcataatggctgaggcagg -3'
(R):5'- CTTCCCAATGAGTGTCAACTAAGG -3'

Posted On

2013-05-09