Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02550:Smarca4'

298054

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Smarca4

Ensembl Gene

ENSMUSG00000032187

Gene Name

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

Synonyms

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

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL02550

Quality Score

Status

Chromosome

Chromosomal Location

21527465-21615526 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 21597418 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Glutamine at position 1391 (P1391Q)

Ref Sequence

ENSEMBL: ENSMUSP00000133922 (fasta)

Gene Model

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

AlphaFold

Q3TKT4

Predicted Effect

probably benign
Transcript: ENSMUST00000034707
AA Change: P1391Q

PolyPhen 2 Score 0.250 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000034707
Gene: ENSMUSG00000032187
AA Change: P1391Q

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 benign
Transcript: ENSMUST00000098948
AA Change: P1394Q

PolyPhen 2 Score 0.201 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000096547
Gene: ENSMUSG00000032187
AA Change: P1394Q

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

unknown
Transcript: ENSMUST00000172996
AA Change: P1231Q

SMART Domains

Protein: ENSMUSP00000133535
Gene: ENSMUSG00000032187
AA Change: P1231Q

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 benign
Transcript: ENSMUST00000174008
AA Change: P1391Q

PolyPhen 2 Score 0.250 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000133922
Gene: ENSMUSG00000032187
AA Change: P1391Q

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

Coding Region Coverage

Validation Efficiency

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acadl	A	G	1: 66,884,325 (GRCm39)		probably null	Het
Acer3	G	A	7: 97,873,185 (GRCm39)	T171I	probably benign	Het
Acsm2	C	T	7: 119,172,507 (GRCm39)	P117S	probably damaging	Het
Anxa2	A	G	9: 69,374,588 (GRCm39)	S22G	probably benign	Het
Arrb2	T	C	11: 70,327,696 (GRCm39)	I120T	probably damaging	Het
Atp11a	G	T	8: 12,866,997 (GRCm39)	K141N	possibly damaging	Het
Casd1	T	C	6: 4,642,009 (GRCm39)	V762A	probably benign	Het
Ccdc61	A	T	7: 18,627,227 (GRCm39)	S48T	probably benign	Het
Cntn2	T	C	1: 132,456,801 (GRCm39)	M82V	probably null	Het
Cobll1	A	G	2: 64,938,207 (GRCm39)	S359P	probably damaging	Het
Ctnnbl1	C	A	2: 157,726,055 (GRCm39)	D465E	probably benign	Het
Def6	A	T	17: 28,447,235 (GRCm39)	E622V	probably benign	Het
Dmgdh	T	C	13: 93,854,083 (GRCm39)	Y678H	probably damaging	Het
Dock9	A	T	14: 121,935,724 (GRCm39)	M1K	probably null	Het
Esyt1	T	C	10: 128,357,962 (GRCm39)	K216E	probably damaging	Het
Fhod3	A	G	18: 25,156,017 (GRCm39)	D545G	probably benign	Het
Galnt12	A	T	4: 47,104,126 (GRCm39)	D128V	possibly damaging	Het
Gm1110	C	T	9: 26,793,130 (GRCm39)	V549I	probably benign	Het
Gm7361	A	G	5: 26,466,120 (GRCm39)	I161V	possibly damaging	Het
Gsn	T	C	2: 35,172,619 (GRCm39)		probably benign	Het
Gvin3	A	T	7: 106,200,846 (GRCm39)		noncoding transcript	Het
Il16	T	A	7: 83,323,704 (GRCm39)	Q282L	possibly damaging	Het
Il3ra	A	G	14: 14,348,055 (GRCm38)	D67G	probably benign	Het
Insrr	T	C	3: 87,711,805 (GRCm39)	L515P	probably damaging	Het
Jhy	A	G	9: 40,828,466 (GRCm39)	F480S	probably benign	Het
Klc4	C	A	17: 46,947,836 (GRCm39)		probably null	Het
Klhl12	G	T	1: 134,395,443 (GRCm39)	C135F	possibly damaging	Het
Ly6m	T	G	15: 74,752,604 (GRCm39)	H24P	probably damaging	Het
Mboat7	G	T	7: 3,686,905 (GRCm39)		probably null	Het
Myo1f	G	A	17: 33,807,116 (GRCm39)	D522N	probably damaging	Het
Myo1f	A	G	17: 33,799,124 (GRCm39)		probably benign	Het
Nbea	C	A	3: 55,926,835 (GRCm39)	M789I	probably damaging	Het
Ncapd2	T	C	6: 125,154,410 (GRCm39)	D602G	probably benign	Het
Ncaph2	A	T	15: 89,254,064 (GRCm39)	K344*	probably null	Het
Nek2	A	G	1: 191,554,371 (GRCm39)	Y70C	probably damaging	Het
Or2t1	T	C	14: 14,328,423 (GRCm38)	L104P	possibly damaging	Het
Or4k35	T	A	2: 111,100,349 (GRCm39)	D121V	probably damaging	Het
Or4k37	T	C	2: 111,158,845 (GRCm39)	L27P	probably damaging	Het
Or5ak22	G	A	2: 85,230,166 (GRCm39)	A237V	probably damaging	Het
Or7e166	C	A	9: 19,624,343 (GRCm39)	F73L	possibly damaging	Het
Or8g35	T	A	9: 39,381,842 (GRCm39)	Y60F	probably benign	Het
Plcb3	T	A	19: 6,937,544 (GRCm39)	K625*	probably null	Het
Plrg1	T	C	3: 82,968,430 (GRCm39)		probably null	Het
Ptpn12	A	G	5: 21,203,137 (GRCm39)	V547A	probably benign	Het
Ralgapb	A	G	2: 158,290,331 (GRCm39)	D748G	probably damaging	Het
Rcbtb2	A	G	14: 73,399,459 (GRCm39)	E41G	probably damaging	Het
Rela	G	T	19: 5,691,534 (GRCm39)	R236L	possibly damaging	Het
Rps6kc1	A	G	1: 190,604,059 (GRCm39)	S188P	probably damaging	Het
Sipa1l1	A	T	12: 82,487,723 (GRCm39)	K1666*	probably null	Het
Slco1a1	C	T	6: 141,889,191 (GRCm39)	M40I	probably benign	Het
Stra6	A	G	9: 58,057,366 (GRCm39)	N392S	possibly damaging	Het
Syt4	A	G	18: 31,577,246 (GRCm39)	I36T	probably damaging	Het
Tgfbr2	A	T	9: 115,939,197 (GRCm39)	M235K	probably benign	Het
Tmem87a	T	A	2: 120,204,966 (GRCm39)		probably null	Het
Tmf1	T	C	6: 97,135,522 (GRCm39)	D918G	probably benign	Het
Tnfaip2	A	G	12: 111,412,535 (GRCm39)	Y312C	probably damaging	Het
Usp47	C	T	7: 111,703,561 (GRCm39)	R1178C	probably damaging	Het
Vmn2r95	T	A	17: 18,671,994 (GRCm39)	I577N	probably damaging	Het
Vps13b	T	C	15: 35,572,242 (GRCm39)	V953A	probably benign	Het
Wasl	A	G	6: 24,633,883 (GRCm39)	F127S	probably damaging	Het
Wdr1	C	T	5: 38,698,206 (GRCm39)	V192I	probably damaging	Het
Wnt9a	C	T	11: 59,221,744 (GRCm39)	T214I	probably damaging	Het
Xpo5	A	G	17: 46,540,255 (GRCm39)	D693G	probably benign	Het
Zan	A	G	5: 137,385,301 (GRCm39)	L5044P	unknown	Het
Zhx3	T	C	2: 160,623,216 (GRCm39)	N317S	probably damaging	Het

Other mutations in Smarca4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01380:Smarca4	APN	9	21,590,369 (GRCm39)	missense	probably benign	0.30
IGL01694:Smarca4	APN	9	21,577,166 (GRCm39)	missense	probably damaging	1.00
IGL02147:Smarca4	APN	9	21,546,999 (GRCm39)	missense	probably damaging	0.98
IGL02417:Smarca4	APN	9	21,612,386 (GRCm39)	missense	probably damaging	1.00
IGL02421:Smarca4	APN	9	21,550,535 (GRCm39)	missense	probably damaging	1.00
IGL02794:Smarca4	APN	9	21,584,638 (GRCm39)	splice site	probably benign
IGL03030:Smarca4	APN	9	21,547,132 (GRCm39)	missense	probably benign	0.14
IGL03037:Smarca4	APN	9	21,544,231 (GRCm39)	unclassified	probably benign
IGL03069:Smarca4	APN	9	21,547,132 (GRCm39)	missense	probably benign	0.14
IGL03355:Smarca4	APN	9	21,547,132 (GRCm39)	missense	probably benign	0.14
R0123:Smarca4	UTSW	9	21,548,620 (GRCm39)	missense	probably damaging	1.00
R0134:Smarca4	UTSW	9	21,548,620 (GRCm39)	missense	probably damaging	1.00
R0230:Smarca4	UTSW	9	21,612,168 (GRCm39)	missense	probably damaging	0.99
R0269:Smarca4	UTSW	9	21,547,497 (GRCm39)	missense	probably benign	0.09
R0631:Smarca4	UTSW	9	21,570,280 (GRCm39)	splice site	probably benign
R0665:Smarca4	UTSW	9	21,612,239 (GRCm39)	small deletion	probably benign
R0726:Smarca4	UTSW	9	21,611,435 (GRCm39)	critical splice donor site	probably null
R0801:Smarca4	UTSW	9	21,553,850 (GRCm39)	missense	possibly damaging	0.81
R0918:Smarca4	UTSW	9	21,547,511 (GRCm39)	missense	probably benign	0.16
R1411:Smarca4	UTSW	9	21,570,251 (GRCm39)	missense	probably damaging	1.00
R1604:Smarca4	UTSW	9	21,612,239 (GRCm39)	small deletion	probably benign
R1768:Smarca4	UTSW	9	21,612,479 (GRCm39)	missense	possibly damaging	0.56
R2004:Smarca4	UTSW	9	21,588,776 (GRCm39)	missense	probably damaging	1.00
R2031:Smarca4	UTSW	9	21,597,358 (GRCm39)	missense	possibly damaging	0.68
R2211:Smarca4	UTSW	9	21,597,325 (GRCm39)	missense	probably damaging	1.00
R2512:Smarca4	UTSW	9	21,546,994 (GRCm39)	missense	possibly damaging	0.95
R2875:Smarca4	UTSW	9	21,553,876 (GRCm39)	missense	possibly damaging	0.55
R3786:Smarca4	UTSW	9	21,583,355 (GRCm39)	missense	possibly damaging	0.94
R4829:Smarca4	UTSW	9	21,550,623 (GRCm39)	missense	probably damaging	0.97
R5084:Smarca4	UTSW	9	21,572,059 (GRCm39)	missense	probably damaging	1.00
R5222:Smarca4	UTSW	9	21,567,002 (GRCm39)	missense	probably benign	0.01
R5785:Smarca4	UTSW	9	21,597,322 (GRCm39)	missense	probably damaging	0.99
R5844:Smarca4	UTSW	9	21,589,238 (GRCm39)	intron	probably benign
R5964:Smarca4	UTSW	9	21,558,726 (GRCm39)	missense	probably benign	0.00
R6001:Smarca4	UTSW	9	21,544,205 (GRCm39)	unclassified	probably benign
R6072:Smarca4	UTSW	9	21,611,417 (GRCm39)	missense	probably damaging	1.00
R6254:Smarca4	UTSW	9	21,611,173 (GRCm39)	missense	probably damaging	1.00
R6320:Smarca4	UTSW	9	21,548,671 (GRCm39)	missense	probably damaging	1.00
R6353:Smarca4	UTSW	9	21,590,445 (GRCm39)	critical splice donor site	probably null
R6461:Smarca4	UTSW	9	21,590,316 (GRCm39)	missense	probably damaging	1.00
R6886:Smarca4	UTSW	9	21,570,127 (GRCm39)	missense	probably damaging	1.00
R7098:Smarca4	UTSW	9	21,546,116 (GRCm39)	missense	probably benign	0.10
R7253:Smarca4	UTSW	9	21,570,256 (GRCm39)	missense	probably benign	0.01
R7307:Smarca4	UTSW	9	21,550,096 (GRCm39)	missense	probably damaging	1.00
R7382:Smarca4	UTSW	9	21,570,229 (GRCm39)	missense	probably damaging	0.98
R7445:Smarca4	UTSW	9	21,597,543 (GRCm39)	missense	probably damaging	1.00
R7535:Smarca4	UTSW	9	21,558,921 (GRCm39)	missense	possibly damaging	0.82
R7573:Smarca4	UTSW	9	21,550,371 (GRCm39)	splice site	probably null
R7644:Smarca4	UTSW	9	21,566,950 (GRCm39)	missense	probably benign	0.00
R7734:Smarca4	UTSW	9	21,578,658 (GRCm39)	missense	possibly damaging	0.65
R7833:Smarca4	UTSW	9	21,558,655 (GRCm39)	missense	possibly damaging	0.86
R8085:Smarca4	UTSW	9	21,570,108 (GRCm39)	splice site	probably null
R8119:Smarca4	UTSW	9	21,558,922 (GRCm39)	missense	possibly damaging	0.61
R8320:Smarca4	UTSW	9	21,588,798 (GRCm39)	missense	probably benign	0.10
R8445:Smarca4	UTSW	9	21,612,239 (GRCm39)	small deletion	probably benign
R8493:Smarca4	UTSW	9	21,570,144 (GRCm39)	missense	probably damaging	1.00
R8748:Smarca4	UTSW	9	21,546,164 (GRCm39)	missense	possibly damaging	0.85
R8788:Smarca4	UTSW	9	21,550,024 (GRCm39)	missense	probably damaging	1.00
R8817:Smarca4	UTSW	9	21,547,497 (GRCm39)	missense	probably benign	0.04
R9241:Smarca4	UTSW	9	21,550,604 (GRCm39)	missense	possibly damaging	0.72
R9446:Smarca4	UTSW	9	21,547,155 (GRCm39)	missense	unknown
R9570:Smarca4	UTSW	9	21,580,849 (GRCm39)	missense	probably damaging	1.00
R9727:Smarca4	UTSW	9	21,611,160 (GRCm39)	missense	probably damaging	1.00
R9801:Smarca4	UTSW	9	21,586,397 (GRCm39)	missense	probably damaging	1.00
Z1176:Smarca4	UTSW	9	21,614,253 (GRCm39)	nonsense	probably null

Posted On

2015-04-16