Mutagenetix > Incidental Mutation

Incidental Mutation 'R1833:Smarcc1'

204969

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

039860-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1833 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

109961129-110069773 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 109982879 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Glutamine at position 204 (H204Q)

Ref Sequence

ENSEMBL: ENSMUSP00000143550 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000088716] [ENSMUST00000197480] [ENSMUST00000197984] [ENSMUST00000199896]

AlphaFold

P97496

Predicted Effect

possibly damaging
Transcript: ENSMUST00000088716
AA Change: H204Q

PolyPhen 2 Score 0.495 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000086094
Gene: ENSMUSG00000032481
AA Change: H204Q

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: ENSMUST00000197480
AA Change: H204Q

PolyPhen 2 Score 0.106 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000142629
Gene: ENSMUSG00000032481
AA Change: H204Q

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000197984
AA Change: H204Q

PolyPhen 2 Score 0.495 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000142611
Gene: ENSMUSG00000032481
AA Change: H204Q

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

possibly damaging
Transcript: ENSMUST00000199896
AA Change: H204Q

PolyPhen 2 Score 0.711 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000143550
Gene: ENSMUSG00000032481
AA Change: H204Q

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: ENSMUST00000200237

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.1%
20x: 91.9%

Validation Efficiency

99% (83/84)

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700003H04Rik	T	A	3: 124,350,509 (GRCm39)	D143V	unknown	Het
4930438A08Rik	C	T	11: 58,179,214 (GRCm39)	Q183*	probably null	Het
9230009I02Rik	A	G	11: 50,982,293 (GRCm39)		noncoding transcript	Het
Abhd12	T	A	2: 150,690,338 (GRCm39)	D119V	probably damaging	Het
Adam1b	A	G	5: 121,641,000 (GRCm39)	I15T	possibly damaging	Het
Agtpbp1	A	T	13: 59,613,797 (GRCm39)		probably null	Het
Arfgef1	G	C	1: 10,275,115 (GRCm39)	I312M	probably benign	Het
Arid4a	C	T	12: 71,122,240 (GRCm39)	L874F	possibly damaging	Het
Bcas3	G	A	11: 85,474,775 (GRCm39)	V317I	probably benign	Het
Ccr1	T	A	9: 123,764,126 (GRCm39)	I135F	probably damaging	Het
Ces2h	A	G	8: 105,747,005 (GRCm39)	E547G	possibly damaging	Het
Ces3b	T	A	8: 105,812,271 (GRCm39)	D173E	probably damaging	Het
Chd3	A	G	11: 69,244,949 (GRCm39)	L1197S	probably damaging	Het
Cngb1	A	G	8: 95,968,983 (GRCm39)	L1175P	probably damaging	Het
Cyp4f17	T	C	17: 32,743,184 (GRCm39)	F286L	probably benign	Het
Dclre1a	C	T	19: 56,529,932 (GRCm39)		probably null	Het
Dennd6a	T	A	14: 26,328,109 (GRCm39)	L44H	probably damaging	Het
Dhx16	A	G	17: 36,196,511 (GRCm39)	T560A	probably benign	Het
Dusp12	T	C	1: 170,702,022 (GRCm39)	M326V	probably benign	Het
Eif3k	T	C	7: 28,670,852 (GRCm39)	I180V	probably benign	Het
Erc1	A	G	6: 119,720,390 (GRCm39)	I437T	possibly damaging	Het
Farp2	T	A	1: 93,504,086 (GRCm39)		probably benign	Het
Foxa3	A	G	7: 18,748,499 (GRCm39)	L209P	probably damaging	Het
Garin2	G	A	12: 78,762,280 (GRCm39)		probably benign	Het
Gen1	A	T	12: 11,298,352 (GRCm39)		probably benign	Het
Gm10305	A	G	4: 99,161,363 (GRCm39)	T91A	unknown	Het
Gm14412	T	C	2: 177,007,583 (GRCm39)	D104G	probably benign	Het
Gm6900	T	C	7: 10,390,515 (GRCm39)		noncoding transcript	Het
Gpx1	A	T	9: 108,216,555 (GRCm39)	Y15F	possibly damaging	Het
H2-M10.3	T	C	17: 36,678,387 (GRCm39)	Y146C	probably damaging	Het
H2-Q7	C	A	17: 35,658,675 (GRCm39)	S104R	probably benign	Het
Hephl1	T	C	9: 14,988,224 (GRCm39)	Y628C	probably damaging	Het
Hspa5	T	A	2: 34,666,065 (GRCm39)	Y636*	probably null	Het
Htt	A	G	5: 35,063,092 (GRCm39)		probably benign	Het
Idh1	T	C	1: 65,200,273 (GRCm39)	I364V	probably benign	Het
Itgae	G	T	11: 73,007,988 (GRCm39)	A423S	possibly damaging	Het
Kng2	T	C	16: 22,830,802 (GRCm39)	N169S	possibly damaging	Het
Larp4b	C	T	13: 9,201,235 (GRCm39)	T369I	possibly damaging	Het
Lcor	T	C	19: 41,573,387 (GRCm39)	I714T	probably benign	Het
Lhfpl7	A	G	5: 113,382,435 (GRCm39)		probably benign	Het
Lonrf2	G	A	1: 38,852,357 (GRCm39)	P165S	probably benign	Het
Magi2	G	T	5: 19,432,455 (GRCm39)	G57C	probably damaging	Het
Mdn1	T	A	4: 32,720,761 (GRCm39)	H2291Q	probably damaging	Het
Mgam	T	C	6: 40,631,652 (GRCm39)		probably null	Het
Micall2	A	G	5: 139,702,508 (GRCm39)	V245A	probably benign	Het
Mipep	T	G	14: 61,109,512 (GRCm39)	Y630D	probably damaging	Het
Msx2	A	T	13: 53,622,221 (GRCm39)	M263K	probably damaging	Het
Nectin2	G	T	7: 19,451,633 (GRCm39)	P467H	probably damaging	Het
Nek10	A	T	14: 14,842,789 (GRCm38)	M165L	probably benign	Het
Nlrp4b	A	T	7: 10,459,863 (GRCm39)	M455L	probably benign	Het
Oaz3	TGGAGGCAGGAGCACGGGAGGCAGGAGCACGGGAGGCAG	TGGAGGCAGGAGCACGGGAGGCAG	3: 94,343,349 (GRCm39)		probably benign	Het
Or10ad1b	T	A	15: 98,124,846 (GRCm39)	I227F	probably damaging	Het
Or4c10	T	A	2: 89,760,645 (GRCm39)	L164*	probably null	Het
Pcx	T	A	19: 4,669,132 (GRCm39)	V710E	probably damaging	Het
Pkn2	C	T	3: 142,527,408 (GRCm39)	R347Q	probably damaging	Het
Pramel51	T	C	12: 88,145,218 (GRCm39)	E44G	possibly damaging	Het
Qsox1	C	T	1: 155,666,791 (GRCm39)	G233S	probably benign	Het
Rbl1	T	A	2: 157,037,475 (GRCm39)	N224I	probably damaging	Het
Rspry1	A	G	8: 95,362,116 (GRCm39)	T132A	probably damaging	Het
Sclt1	A	G	3: 41,681,546 (GRCm39)	V91A	probably damaging	Het
Sema4f	A	T	6: 82,895,540 (GRCm39)	L331H	probably benign	Het
Sf3b3	T	A	8: 111,544,198 (GRCm39)	Q814L	probably benign	Het
Slc19a2	T	G	1: 164,089,753 (GRCm39)	Y190D	probably damaging	Het
Sox6	T	C	7: 115,376,328 (GRCm39)	K135E	probably damaging	Het
Tecpr1	T	C	5: 144,145,426 (GRCm39)	Q607R	probably damaging	Het
Tgfb1i1	A	G	7: 127,848,670 (GRCm39)		probably benign	Het
Tirap	T	G	9: 35,099,999 (GRCm39)	R228S	probably benign	Het
Trp53bp2	T	A	1: 182,256,581 (GRCm39)	H50Q	probably damaging	Het
Try4	A	G	6: 41,280,365 (GRCm39)	H63R	probably damaging	Het
Vmn2r25	G	A	6: 123,816,643 (GRCm39)	P313S	probably benign	Het
Vps26a	A	C	10: 62,294,825 (GRCm39)	L250V	probably benign	Het
Vwf	A	G	6: 125,619,000 (GRCm39)	H1226R	probably benign	Het
Wdtc1	TCC	TC	4: 133,036,053 (GRCm39)		probably benign	Het
Zc3hav1l	A	T	6: 38,274,881 (GRCm39)		probably benign	Het
Zfp119b	T	G	17: 56,246,271 (GRCm39)	H305P	probably damaging	Het
Zfp326	C	T	5: 106,039,035 (GRCm39)	Q134*	probably null	Het
Zfp975	C	T	7: 42,311,263 (GRCm39)	R450Q	probably benign	Het
Zfyve26	A	T	12: 79,333,032 (GRCm39)	M313K	probably benign	Het
Zscan5b	T	C	7: 6,241,965 (GRCm39)	S395P	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
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
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'- CAGGCATCTGAAACACTTGATAAAG -3'
(R):5'- CCAGCTAAGTGATACGTTAGAGAAAAC -3'

Sequencing Primer
(F):5'- CACTATCCCTTTGCTTGACA -3'
(R):5'- CAGAACTCTATGGAAATGGTGGTG -3'

Posted On

2014-06-23