Mutagenetix > Incidental Mutation

Incidental Mutation 'R7307:Smarca4'

567318

Institutional Source

Beutler Lab

Gene Symbol

Smarca4

Ensembl Gene

ENSMUSG00000032187

Gene Name

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4

Synonyms

SNF2beta, SW1/SNF, b2b508.1Clo, Brg1, b2b692Clo

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7307 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

21616169-21704230 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 21638800 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 402 (I402N)

Ref Sequence

ENSEMBL: ENSMUSP00000096547 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034707] [ENSMUST00000098948] [ENSMUST00000174008]

AlphaFold

Q3TKT4

Predicted Effect

probably damaging
Transcript: ENSMUST00000034707
AA Change: I402N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000034707
Gene: ENSMUSG00000032187
AA Change: I402N

Domain	Start	End	E-Value	Type
low complexity region	6	58	N/A	INTRINSIC
low complexity region	130	153	N/A	INTRINSIC
QLQ	170	206	3.98e-14	SMART
low complexity region	221	247	N/A	INTRINSIC
low complexity region	252	289	N/A	INTRINSIC
low complexity region	304	330	N/A	INTRINSIC
low complexity region	407	418	N/A	INTRINSIC
HSA	460	532	2e-27	SMART
coiled coil region	563	595	N/A	INTRINSIC
BRK	612	656	5.17e-21	SMART
low complexity region	657	672	N/A	INTRINSIC
low complexity region	691	702	N/A	INTRINSIC
DEXDc	750	942	5.17e-38	SMART
Blast:DEXDc	953	985	7e-10	BLAST
low complexity region	1019	1034	N/A	INTRINSIC
HELICc	1110	1194	7.27e-24	SMART
low complexity region	1252	1267	N/A	INTRINSIC
SnAC	1288	1356	2.8e-29	SMART
low complexity region	1360	1385	N/A	INTRINSIC
low complexity region	1388	1398	N/A	INTRINSIC
BROMO	1422	1533	4.19e-42	SMART
low complexity region	1534	1557	N/A	INTRINSIC
low complexity region	1578	1588	N/A	INTRINSIC
low complexity region	1594	1614	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000098948
AA Change: I402N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000096547
Gene: ENSMUSG00000032187
AA Change: I402N

Domain	Start	End	E-Value	Type
low complexity region	6	58	N/A	INTRINSIC
low complexity region	130	153	N/A	INTRINSIC
QLQ	170	206	3.98e-14	SMART
low complexity region	221	247	N/A	INTRINSIC
low complexity region	252	289	N/A	INTRINSIC
low complexity region	304	330	N/A	INTRINSIC
low complexity region	407	418	N/A	INTRINSIC
HSA	460	532	2e-27	SMART
coiled coil region	563	595	N/A	INTRINSIC
BRK	612	656	5.17e-21	SMART
low complexity region	657	672	N/A	INTRINSIC
low complexity region	691	702	N/A	INTRINSIC
DEXDc	750	942	5.17e-38	SMART
Blast:DEXDc	953	985	7e-10	BLAST
low complexity region	1019	1034	N/A	INTRINSIC
HELICc	1110	1194	7.27e-24	SMART
low complexity region	1252	1267	N/A	INTRINSIC
SnAC	1288	1356	2.8e-29	SMART
low complexity region	1363	1388	N/A	INTRINSIC
low complexity region	1391	1401	N/A	INTRINSIC
BROMO	1425	1536	4.19e-42	SMART
low complexity region	1537	1560	N/A	INTRINSIC
low complexity region	1581	1591	N/A	INTRINSIC
low complexity region	1597	1617	N/A	INTRINSIC

Predicted Effect

SMART Domains

Protein: ENSMUSP00000133535
Gene: ENSMUSG00000032187
AA Change: I206N

Domain	Start	End	E-Value	Type
low complexity region	26	52	N/A	INTRINSIC
low complexity region	57	94	N/A	INTRINSIC
low complexity region	109	135	N/A	INTRINSIC
low complexity region	212	223	N/A	INTRINSIC
HSA	265	337	2e-27	SMART
coiled coil region	367	399	N/A	INTRINSIC
BRK	417	461	5.17e-21	SMART
low complexity region	462	477	N/A	INTRINSIC
low complexity region	496	507	N/A	INTRINSIC
DEXDc	555	747	5.17e-38	SMART
Blast:DEXDc	758	790	6e-10	BLAST
low complexity region	824	839	N/A	INTRINSIC
HELICc	915	999	7.27e-24	SMART
low complexity region	1088	1105	N/A	INTRINSIC
SnAC	1126	1194	2.8e-29	SMART
low complexity region	1201	1226	N/A	INTRINSIC
low complexity region	1229	1239	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000174008
AA Change: I402N

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000133922
Gene: ENSMUSG00000032187
AA Change: I402N

Domain	Start	End	E-Value	Type
low complexity region	6	58	N/A	INTRINSIC
low complexity region	130	153	N/A	INTRINSIC
QLQ	170	206	3.98e-14	SMART
low complexity region	221	247	N/A	INTRINSIC
low complexity region	252	289	N/A	INTRINSIC
low complexity region	304	330	N/A	INTRINSIC
low complexity region	407	418	N/A	INTRINSIC
HSA	460	532	2e-27	SMART
coiled coil region	563	595	N/A	INTRINSIC
BRK	612	656	5.17e-21	SMART
low complexity region	657	672	N/A	INTRINSIC
low complexity region	691	702	N/A	INTRINSIC
DEXDc	750	942	5.17e-38	SMART
Blast:DEXDc	953	985	7e-10	BLAST
low complexity region	1019	1034	N/A	INTRINSIC
HELICc	1110	1194	7.27e-24	SMART
low complexity region	1252	1267	N/A	INTRINSIC
SnAC	1288	1356	2.8e-29	SMART
low complexity region	1360	1385	N/A	INTRINSIC
low complexity region	1388	1398	N/A	INTRINSIC
BROMO	1422	1532	1.36e-41	SMART
low complexity region	1533	1556	N/A	INTRINSIC
low complexity region	1577	1587	N/A	INTRINSIC
low complexity region	1593	1613	N/A	INTRINSIC

Meta Mutation Damage Score

0.8370

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (75/75)

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 and is similar to the brahma protein of Drosophila. Members of this family have helicase and ATPase activities and 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, which is required for transcriptional activation of genes normally repressed by chromatin. In addition, this protein can bind BRCA1, as well as regulate the expression of the tumorigenic protein CD44. Mutations in this gene cause rhabdoid tumor predisposition syndrome type 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]
PHENOTYPE: Homozygotes for a null allele die in utero before implantation. Embryos heterozygous for this null allele and an ENU-induced allele show impaired definitive erythropoiesis, anemia and lethality during organogenesis. Heterozygotes for a different null allele show cyanosis and cardiovascular defects. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610318N02Rik	G	A	16: 17,118,395	P155L	probably benign	Het
Adamts12	G	T	15: 11,217,813	L285F	probably damaging	Het
Ankrd6	A	T	4: 32,816,949	Y393N	possibly damaging	Het
Arhgap45	A	G	10: 80,029,182	Q993R	probably benign	Het
Arhgef33	G	C	17: 80,347,120		probably null	Het
B4galnt3	T	C	6: 120,215,431	D448G	probably benign	Het
Capn1	C	G	19: 5,993,908	E564D	possibly damaging	Het
Ccdc85a	A	G	11: 28,399,384	S474P	probably benign	Het
Cdk12	T	A	11: 98,249,800	L1289*	probably null	Het
Cramp1l	A	T	17: 24,974,745	N920K	possibly damaging	Het
Cubn	C	T	2: 13,340,332	S2091N	probably damaging	Het
Ddx1	A	T	12: 13,223,959	I581N	probably damaging	Het
Dnm2	A	T	9: 21,485,687	N487Y	probably damaging	Het
Enc1	A	C	13: 97,245,093	N37T	probably damaging	Het
Ephb3	T	G	16: 21,222,226	I932S	probably benign	Het
Frk	T	A	10: 34,591,938	M316K	probably damaging	Het
Gdap2	C	T	3: 100,202,033	R25C	unknown	Het
Gm10436	A	C	12: 88,181,749	C32W	probably damaging	Het
Gpat2	T	A	2: 127,434,890	D671E	probably damaging	Het
Gpr179	C	T	11: 97,338,846	E828K	probably benign	Het
Greb1l	T	C	18: 10,538,142	Y1052H	probably damaging	Het
Gtf2f1	C	T	17: 57,007,833	S69N	probably damaging	Het
Hid1	A	C	11: 115,348,482	I785S	probably damaging	Het
Hmcn2	T	C	2: 31,343,081	I214T	probably damaging	Het
Hsd3b5	G	T	3: 98,619,769	F120L	probably damaging	Het
Kif16b	C	T	2: 142,712,931	R649Q	probably benign	Het
Kif17	A	T	4: 138,262,643	E47D	probably benign	Het
Kmt2b	T	C	7: 30,580,471	H1368R	probably damaging	Het
Kmt2d	A	T	15: 98,849,418	S3342T	unknown	Het
Krt82	A	G	15: 101,542,907	C356R	probably damaging	Het
Lrit2	A	G	14: 37,072,199	K407E	probably benign	Het
Malt1	T	A	18: 65,451,569	H325Q	possibly damaging	Het
Mccc2	T	G	13: 99,988,600	D187A	possibly damaging	Het
Mgll	T	A	6: 88,814,121		probably null	Het
Mindy2	T	G	9: 70,610,959	E449A	possibly damaging	Het
Muc5b	G	A	7: 141,842,294	V96M	unknown	Het
Nlrp4e	A	G	7: 23,321,528	E480G	probably benign	Het
Nup98	A	G	7: 102,134,795	I1093T	probably benign	Het
Olfr1288	A	T	2: 111,478,760		probably benign	Het
Olfr243	G	T	7: 103,716,966	R124L	probably damaging	Het
Olfr350	G	A	2: 36,850,125	M26I	probably benign	Het
Olfr541	G	A	7: 140,705,147	V299I	probably benign	Het
Pcdhb6	A	T	18: 37,335,478	H484L	probably benign	Het
Phldb1	T	C	9: 44,694,047	T604A	possibly damaging	Het
Pitpnm3	G	T	11: 72,070,964	A275D	probably damaging	Het
Polr2a	A	T	11: 69,747,292		probably null	Het
Polr3a	A	G	14: 24,459,987	C960R	probably benign	Het
Pou6f2	G	A	13: 18,239,713	A159V		Het
Pramef6	A	C	4: 143,896,775	Y276*	probably null	Het
Psmc4	A	G	7: 28,042,660	V303A	probably benign	Het
Ptdss2	A	G	7: 141,151,732	N151S	possibly damaging	Het
Ptprk	T	A	10: 28,589,008	Y1295*	probably null	Het
Rbm19	A	G	5: 120,186,218	K881E	possibly damaging	Het
Rcan2	T	A	17: 44,021,102	Y183*	probably null	Het
Rnd1	T	C	15: 98,670,799	E166G	probably damaging	Het
Rnf113a2	T	A	12: 84,418,179	C282S	probably damaging	Het
S100b	G	A	10: 76,257,092	G20R	probably benign	Het
Sae1	G	T	7: 16,368,544	Y168*	probably null	Het
Samd9l	C	A	6: 3,372,600	G1554*	probably null	Het
Samhd1	T	C	2: 157,135,020	S55G	probably benign	Het
Sgsm1	T	C	5: 113,273,646	D525G	probably benign	Het
Slc28a3	A	T	13: 58,563,172	M512K	probably damaging	Het
Slc9b2	T	A	3: 135,318,390	N67K	probably benign	Het
St7l	T	C	3: 104,889,353	F261L	probably benign	Het
Syde2	T	A	3: 146,015,798	V1140D	probably damaging	Het
Syt6	T	A	3: 103,587,472	I251N	probably damaging	Het
Taok2	T	C	7: 126,866,818	E916G	probably damaging	Het
Tecta	A	G	9: 42,377,992	S426P	probably damaging	Het
Thra	T	C	11: 98,764,308	I338T	probably damaging	Het
Trub1	A	T	19: 57,472,703	Y137F	probably damaging	Het
Vps13b	T	C	15: 35,841,545	F2574L	probably benign	Het
Ythdf3	T	C	3: 16,183,500	S2P	possibly damaging	Het
Zc3h13	T	A	14: 75,330,541	D1091E	probably damaging	Het
Zdhhc6	A	G	19: 55,313,250	Y100H	probably damaging	Het

Other mutations in Smarca4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01380:Smarca4	APN	9	21679073	missense	probably benign	0.30
IGL01694:Smarca4	APN	9	21665870	missense	probably damaging	1.00
IGL02147:Smarca4	APN	9	21635703	missense	probably damaging	0.98
IGL02417:Smarca4	APN	9	21701090	missense	probably damaging	1.00
IGL02421:Smarca4	APN	9	21639239	missense	probably damaging	1.00
IGL02550:Smarca4	APN	9	21686122	missense	probably benign	0.25
IGL02794:Smarca4	APN	9	21673342	splice site	probably benign
IGL03030:Smarca4	APN	9	21635836	missense	probably benign	0.14
IGL03037:Smarca4	APN	9	21632935	unclassified	probably benign
IGL03069:Smarca4	APN	9	21635836	missense	probably benign	0.14
IGL03355:Smarca4	APN	9	21635836	missense	probably benign	0.14
R0123:Smarca4	UTSW	9	21637324	missense	probably damaging	1.00
R0134:Smarca4	UTSW	9	21637324	missense	probably damaging	1.00
R0230:Smarca4	UTSW	9	21700872	missense	probably damaging	0.99
R0269:Smarca4	UTSW	9	21636201	missense	probably benign	0.09
R0631:Smarca4	UTSW	9	21658984	splice site	probably benign
R0665:Smarca4	UTSW	9	21700943	small deletion	probably benign
R0726:Smarca4	UTSW	9	21700139	critical splice donor site	probably null
R0801:Smarca4	UTSW	9	21642554	missense	possibly damaging	0.81
R0918:Smarca4	UTSW	9	21636215	missense	probably benign	0.16
R1411:Smarca4	UTSW	9	21658955	missense	probably damaging	1.00
R1604:Smarca4	UTSW	9	21700943	small deletion	probably benign
R1768:Smarca4	UTSW	9	21701183	missense	possibly damaging	0.56
R2004:Smarca4	UTSW	9	21677480	missense	probably damaging	1.00
R2031:Smarca4	UTSW	9	21686062	missense	possibly damaging	0.68
R2211:Smarca4	UTSW	9	21686029	missense	probably damaging	1.00
R2512:Smarca4	UTSW	9	21635698	missense	possibly damaging	0.95
R2875:Smarca4	UTSW	9	21642580	missense	possibly damaging	0.55
R3786:Smarca4	UTSW	9	21672059	missense	possibly damaging	0.94
R4829:Smarca4	UTSW	9	21639327	missense	probably damaging	0.97
R5084:Smarca4	UTSW	9	21660763	missense	probably damaging	1.00
R5222:Smarca4	UTSW	9	21655706	missense	probably benign	0.01
R5785:Smarca4	UTSW	9	21686026	missense	probably damaging	0.99
R5844:Smarca4	UTSW	9	21677942	intron	probably benign
R5964:Smarca4	UTSW	9	21647430	missense	probably benign	0.00
R6001:Smarca4	UTSW	9	21632909	unclassified	probably benign
R6072:Smarca4	UTSW	9	21700121	missense	probably damaging	1.00
R6254:Smarca4	UTSW	9	21699877	missense	probably damaging	1.00
R6320:Smarca4	UTSW	9	21637375	missense	probably damaging	1.00
R6353:Smarca4	UTSW	9	21679149	critical splice donor site	probably null
R6461:Smarca4	UTSW	9	21679020	missense	probably damaging	1.00
R6886:Smarca4	UTSW	9	21658831	missense	probably damaging	1.00
R7098:Smarca4	UTSW	9	21634820	missense	probably benign	0.10
R7253:Smarca4	UTSW	9	21658960	missense	probably benign	0.01
R7382:Smarca4	UTSW	9	21658933	missense	probably damaging	0.98
R7445:Smarca4	UTSW	9	21686247	missense	probably damaging	1.00
R7535:Smarca4	UTSW	9	21647625	missense	possibly damaging	0.82
R7573:Smarca4	UTSW	9	21639075	splice site	probably null
R7644:Smarca4	UTSW	9	21655654	missense	probably benign	0.00
R7734:Smarca4	UTSW	9	21667362	missense	possibly damaging	0.65
R7833:Smarca4	UTSW	9	21647359	missense	possibly damaging	0.86
R8085:Smarca4	UTSW	9	21658812	splice site	probably null
R8119:Smarca4	UTSW	9	21647626	missense	possibly damaging	0.61
R8320:Smarca4	UTSW	9	21677502	missense	probably benign	0.10
R8445:Smarca4	UTSW	9	21700943	small deletion	probably benign
R8493:Smarca4	UTSW	9	21658848	missense	probably damaging	1.00
R8748:Smarca4	UTSW	9	21634868	missense	possibly damaging	0.85
R8788:Smarca4	UTSW	9	21638728	missense	probably damaging	1.00
R8817:Smarca4	UTSW	9	21636201	missense	probably benign	0.04
R9241:Smarca4	UTSW	9	21639308	missense	possibly damaging	0.72
R9446:Smarca4	UTSW	9	21635859	missense	unknown
R9570:Smarca4	UTSW	9	21669553	missense	probably damaging	1.00
R9727:Smarca4	UTSW	9	21699864	missense	probably damaging	1.00
R9801:Smarca4	UTSW	9	21675101	missense	probably damaging	1.00
Z1176:Smarca4	UTSW	9	21702957	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- CTGCCTCCTTTCAGGGATAG -3'
(R):5'- GCTATGCAAGGCCAAGTCTTG -3'

Sequencing Primer
(F):5'- GGGATAGATTCTTCATAGACTCTAGC -3'
(R):5'- AGGCCAAGTCTTGCCACAG -3'

Posted On

2019-06-26