Mutagenetix > Incidental Mutation

Incidental Mutation 'R2058:Smarcc1'

228382

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

040063-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2058 (G1)

Quality Score

196

Status

Validated

Chromosome

Chromosomal Location

109961129-110069773 bp(+) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

A to G at 109947411 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000143700 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000098355] [ENSMUST00000111991] [ENSMUST00000165596] [ENSMUST00000196171] [ENSMUST00000196497] [ENSMUST00000200066] [ENSMUST00000198425] [ENSMUST00000197928] [ENSMUST00000200476] [ENSMUST00000199529] [ENSMUST00000197182] [ENSMUST00000199835]

AlphaFold

P97496

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000082943

Predicted Effect

probably benign
Transcript: ENSMUST00000098355

SMART Domains

Protein: ENSMUSP00000095958
Gene: ENSMUSG00000032481

Domain	Start	End	E-Value	Type
low complexity region	62	71	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000111991

SMART Domains

Protein: ENSMUSP00000107622
Gene: ENSMUSG00000032480

Domain	Start	End	E-Value	Type
internal_repeat_1	47	94	6.21e-5	PROSPERO
low complexity region	188	199	N/A	INTRINSIC
internal_repeat_1	239	285	6.21e-5	PROSPERO
low complexity region	292	313	N/A	INTRINSIC
DEXDc	432	621	9.66e-29	SMART
low complexity region	650	660	N/A	INTRINSIC
HELICc	682	787	1.63e-17	SMART
HA2	850	940	5.16e-22	SMART
Pfam:OB_NTP_bind	952	1106	2.1e-7	PFAM
low complexity region	1171	1179	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000165596

SMART Domains

Protein: ENSMUSP00000129174
Gene: ENSMUSG00000032480

Domain	Start	End	E-Value	Type
internal_repeat_1	70	117	6.77e-5	PROSPERO
low complexity region	211	222	N/A	INTRINSIC
internal_repeat_1	262	308	6.77e-5	PROSPERO
low complexity region	315	336	N/A	INTRINSIC
DEXDc	455	644	9.66e-29	SMART
low complexity region	673	683	N/A	INTRINSIC
HELICc	705	810	1.63e-17	SMART
HA2	873	963	5.16e-22	SMART
Pfam:OB_NTP_bind	975	1129	1.8e-7	PFAM
low complexity region	1194	1202	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000196171

SMART Domains

Protein: ENSMUSP00000143616
Gene: ENSMUSG00000032480

Domain	Start	End	E-Value	Type
internal_repeat_1	39	86	5.84e-5	PROSPERO
low complexity region	180	191	N/A	INTRINSIC
internal_repeat_1	231	277	5.84e-5	PROSPERO
low complexity region	284	305	N/A	INTRINSIC
DEXDc	424	613	9.66e-29	SMART
low complexity region	642	652	N/A	INTRINSIC
HELICc	674	779	1.63e-17	SMART
HA2	842	932	5.16e-22	SMART
Pfam:OB_NTP_bind	947	1097	2.8e-9	PFAM
low complexity region	1163	1171	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000196497

SMART Domains

Protein: ENSMUSP00000143529
Gene: ENSMUSG00000032480

Domain	Start	End	E-Value	Type
PDB:2DB2\|A	67	101	5e-18	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196788

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000197785

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196828

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000197979

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000198843

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199801

Predicted Effect

probably benign
Transcript: ENSMUST00000200066

SMART Domains

Protein: ENSMUSP00000143371
Gene: ENSMUSG00000032480

Domain	Start	End	E-Value	Type
internal_repeat_1	47	94	6.21e-5	PROSPERO
low complexity region	188	199	N/A	INTRINSIC
internal_repeat_1	239	285	6.21e-5	PROSPERO
low complexity region	292	313	N/A	INTRINSIC
DEXDc	432	621	9.66e-29	SMART
low complexity region	650	660	N/A	INTRINSIC
HELICc	682	787	1.63e-17	SMART
HA2	850	940	5.16e-22	SMART
Pfam:OB_NTP_bind	952	1106	2.1e-7	PFAM
low complexity region	1171	1179	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000198425

SMART Domains

Protein: ENSMUSP00000142659
Gene: ENSMUSG00000032480

Domain	Start	End	E-Value	Type
internal_repeat_1	70	117	6.77e-5	PROSPERO
low complexity region	211	222	N/A	INTRINSIC
internal_repeat_1	262	308	6.77e-5	PROSPERO
low complexity region	315	336	N/A	INTRINSIC
DEXDc	455	644	9.66e-29	SMART
low complexity region	673	683	N/A	INTRINSIC
HELICc	705	810	1.63e-17	SMART
HA2	873	963	5.16e-22	SMART
Pfam:OB_NTP_bind	975	1129	1.8e-7	PFAM
low complexity region	1194	1202	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000197928

SMART Domains

Protein: ENSMUSP00000142549
Gene: ENSMUSG00000032480

Domain	Start	End	E-Value	Type
internal_repeat_1	47	94	6.21e-5	PROSPERO
low complexity region	188	199	N/A	INTRINSIC
internal_repeat_1	239	285	6.21e-5	PROSPERO
low complexity region	292	313	N/A	INTRINSIC
DEXDc	432	621	9.66e-29	SMART
low complexity region	650	660	N/A	INTRINSIC
HELICc	682	787	1.63e-17	SMART
HA2	850	940	5.16e-22	SMART
Pfam:OB_NTP_bind	952	1106	2.1e-7	PFAM
low complexity region	1171	1179	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000200476

Predicted Effect

probably benign
Transcript: ENSMUST00000199529

SMART Domains

Protein: ENSMUSP00000142489
Gene: ENSMUSG00000032480

Domain	Start	End	E-Value	Type
internal_repeat_1	47	94	6.21e-5	PROSPERO
low complexity region	188	199	N/A	INTRINSIC
internal_repeat_1	239	285	6.21e-5	PROSPERO
low complexity region	292	313	N/A	INTRINSIC
DEXDc	432	621	9.66e-29	SMART
low complexity region	650	660	N/A	INTRINSIC
HELICc	682	787	1.63e-17	SMART
HA2	850	940	5.16e-22	SMART
Pfam:OB_NTP_bind	952	1106	2.1e-7	PFAM
low complexity region	1171	1179	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000197182

Predicted Effect

probably benign
Transcript: ENSMUST00000199835

SMART Domains

Protein: ENSMUSP00000142636
Gene: ENSMUSG00000032480

Domain	Start	End	E-Value	Type
PDB:2DB2\|A	67	171	3e-68	PDB
SCOP:d1di2a_	76	145	3e-3	SMART

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.1%
20x: 94.6%

Validation Efficiency

99% (94/95)

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: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam18	A	T	8: 25,162,082 (GRCm39)		probably benign	Het
Adgrf5	A	G	17: 43,739,477 (GRCm39)	Y72C	possibly damaging	Het
Alas1	T	C	9: 106,118,489 (GRCm39)	E211G	probably damaging	Het
Alkbh1	C	T	12: 87,490,520 (GRCm39)		probably benign	Het
Ano1	A	G	7: 144,201,789 (GRCm39)	V334A	probably damaging	Het
Arhgap18	C	T	10: 26,730,904 (GRCm39)	T122I	probably benign	Het
Arhgef4	A	G	1: 34,761,458 (GRCm39)	K238R	unknown	Het
Atf6b	A	T	17: 34,867,549 (GRCm39)		probably null	Het
Atp2a1	G	A	7: 126,046,844 (GRCm39)	A847V	possibly damaging	Het
Baz1b	T	A	5: 135,246,079 (GRCm39)	N509K	probably benign	Het
BC051076	A	T	5: 88,111,844 (GRCm39)		noncoding transcript	Het
Cage1	A	G	13: 38,207,356 (GRCm39)	V163A	probably benign	Het
Canx	T	C	11: 50,195,252 (GRCm39)	N272S	probably damaging	Het
Cd302	T	A	2: 60,082,767 (GRCm39)	I186F	possibly damaging	Het
Cd84	A	G	1: 171,700,317 (GRCm39)	T145A	possibly damaging	Het
Cep112	T	A	11: 108,410,087 (GRCm39)		probably null	Het
Cmtm4	A	C	8: 105,081,920 (GRCm39)	F156V	probably damaging	Het
Col4a1	T	A	8: 11,260,792 (GRCm39)	D1330V	probably damaging	Het
Ctsa	T	G	2: 164,676,822 (GRCm39)	M136R	probably null	Het
Cyp2d10	T	A	15: 82,288,015 (GRCm39)	I363F	probably damaging	Het
Dmbt1	G	A	7: 130,707,900 (GRCm39)	A1381T	possibly damaging	Het
Dmwd	T	A	7: 18,814,652 (GRCm39)	L434Q	probably damaging	Het
Fat4	T	A	3: 38,945,319 (GRCm39)	M1404K	possibly damaging	Het
Gcc2	T	A	10: 58,121,779 (GRCm39)	S1102T	probably benign	Het
Gcm2	T	C	13: 41,263,430 (GRCm39)	M1V	probably null	Het
Gna14	G	C	19: 16,585,505 (GRCm39)		probably benign	Het
Gsk3b	T	A	16: 38,008,271 (GRCm39)	D192E	probably benign	Het
Gulo	A	G	14: 66,228,608 (GRCm39)	V270A	possibly damaging	Het
Hps5	T	A	7: 46,417,475 (GRCm39)	D904V	probably damaging	Het
Il7	A	T	3: 7,638,975 (GRCm39)	N130K	probably damaging	Het
Jak3	A	T	8: 72,138,027 (GRCm39)		probably null	Het
Klhl6	T	G	16: 19,801,681 (GRCm39)	T25P	probably benign	Het
Kremen2	T	C	17: 23,961,691 (GRCm39)	E272G	possibly damaging	Het
Map3k21	A	G	8: 126,665,461 (GRCm39)	K550R	probably benign	Het
Mphosph10	T	A	7: 64,026,499 (GRCm39)	L650F	probably damaging	Het
Mrpl48	T	C	7: 100,198,540 (GRCm39)	E204G	probably damaging	Het
Msh5	A	C	17: 35,248,732 (GRCm39)	V738G	probably damaging	Het
Mybph	G	A	1: 134,127,857 (GRCm39)	C473Y	probably damaging	Het
Nid1	A	C	13: 13,675,058 (GRCm39)	H926P	probably benign	Het
Nlrp9a	T	A	7: 26,256,787 (GRCm39)	I46K	possibly damaging	Het
Notch3	T	C	17: 32,362,618 (GRCm39)	T1336A	probably benign	Het
Nsun4	T	C	4: 115,910,877 (GRCm39)		probably null	Het
Or1e30	A	G	11: 73,678,100 (GRCm39)	N112S	probably benign	Het
Or5m10	A	T	2: 85,717,296 (GRCm39)	T51S	possibly damaging	Het
Osgin1	A	G	8: 120,172,412 (GRCm39)	D402G	possibly damaging	Het
Patl1	A	G	19: 11,909,511 (GRCm39)	E479G	possibly damaging	Het
Pbsn	T	C	X: 76,891,582 (GRCm39)	K72E	probably damaging	Het
Pcdhb13	A	G	18: 37,577,620 (GRCm39)	Q666R	possibly damaging	Het
Pi4k2b	G	A	5: 52,908,022 (GRCm39)	V131I	probably benign	Het
Pkn2	G	A	3: 142,559,232 (GRCm39)	H98Y	possibly damaging	Het
Pms1	A	G	1: 53,314,327 (GRCm39)	Y73H	probably benign	Het
Ppt2	A	T	17: 34,841,818 (GRCm39)		probably benign	Het
Prkdc	A	G	16: 15,545,469 (GRCm39)	T1862A	probably benign	Het
Prl6a1	T	C	13: 27,503,081 (GRCm39)	Y231H	probably benign	Het
Ranbp3l	T	A	15: 9,029,641 (GRCm39)	V41D	probably damaging	Het
Rhobtb2	T	C	14: 70,031,488 (GRCm39)	T546A	possibly damaging	Het
Ripk4	A	T	16: 97,545,342 (GRCm39)	L372*	probably null	Het
Rnf126	A	G	10: 79,594,971 (GRCm39)		probably benign	Het
S100pbp	A	G	4: 129,075,893 (GRCm39)	V144A	probably benign	Het
Saal1	T	C	7: 46,348,880 (GRCm39)	Q317R	probably damaging	Het
Sap25	G	A	5: 137,641,034 (GRCm39)	G277R	probably damaging	Het
Senp2	C	T	16: 21,832,949 (GRCm39)	T79I	probably damaging	Het
Serpinb9c	A	T	13: 33,340,854 (GRCm39)	C81*	probably null	Het
Set	A	G	2: 29,959,048 (GRCm39)	K70E	possibly damaging	Het
Setd3	A	G	12: 108,073,600 (GRCm39)	I559T	probably benign	Het
Sik1	A	G	17: 32,067,771 (GRCm39)	S435P	probably benign	Het
Skint3	A	T	4: 112,112,980 (GRCm39)	K197*	probably null	Het
Skint5	T	A	4: 113,727,897 (GRCm39)	I402F	possibly damaging	Het
Slc18a1	G	A	8: 69,496,613 (GRCm39)	T350M	probably damaging	Het
Slc19a3	A	T	1: 82,992,512 (GRCm39)	I403K	probably damaging	Het
Slc1a7	C	T	4: 107,861,636 (GRCm39)	T225I	probably benign	Het
Slc38a4	T	C	15: 96,906,606 (GRCm39)	I336V	probably benign	Het
St8sia5	A	T	18: 77,342,459 (GRCm39)	I390F	probably damaging	Het
Strc	A	T	2: 121,209,368 (GRCm39)	W290R	probably damaging	Het
Svep1	T	C	4: 58,084,554 (GRCm39)	D1858G	possibly damaging	Het
Sympk	G	A	7: 18,777,454 (GRCm39)	R568Q	probably damaging	Het
Tex44	A	C	1: 86,354,728 (GRCm39)	K212N	probably damaging	Het
Tgm4	T	C	9: 122,890,835 (GRCm39)	I54T	probably damaging	Het
Thrap3	C	T	4: 126,073,967 (GRCm39)	V260I	probably damaging	Het
Thsd7a	A	T	6: 12,318,105 (GRCm39)		probably benign	Het
Trim12c	A	G	7: 103,997,398 (GRCm39)	F53L	possibly damaging	Het
Ttc6	T	A	12: 57,784,479 (GRCm39)	D1849E	probably benign	Het
Ubap2l	A	T	3: 89,938,683 (GRCm39)		probably benign	Het
Umodl1	G	A	17: 31,227,740 (GRCm39)		probably null	Het
Usp17la	A	C	7: 104,510,378 (GRCm39)	T328P	probably damaging	Het
Vmn2r113	T	A	17: 23,177,223 (GRCm39)	L669*	probably null	Het
Vps13b	T	A	15: 35,841,593 (GRCm39)	V2541E	probably damaging	Het
Wnt3	T	C	11: 103,703,111 (GRCm39)	I198T	probably damaging	Het
Zfp316	T	C	5: 143,249,161 (GRCm39)	E158G	unknown	Het
Zfp362	T	G	4: 128,680,780 (GRCm39)	I182L	possibly damaging	Het
Zfp804a	A	G	2: 82,087,710 (GRCm39)	D513G	probably benign	Het
Zfp879	C	T	11: 50,723,428 (GRCm39)	E543K	probably benign	Het
Zfp97	T	A	17: 17,365,018 (GRCm39)	N172K	possibly damaging	Het
Zmym6	A	T	4: 126,982,208 (GRCm39)	K82*	probably null	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
R0403:Smarcc1	UTSW	9	110,066,876 (GRCm39)	splice site	probably null
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
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'- TGGGCAGTAGTTCACAGCTG -3'
(R):5'- CTGAAGTCACCTGTGCTGTG -3'

Sequencing Primer
(F):5'- GACAATATTTGAGGATGTGCCC -3'
(R):5'- CAGTGGTTATGAACACTTGCC -3'

Posted On

2014-09-17