Mutagenetix > Incidental Mutation

Incidental Mutation 'R4552:Arid1a'

377804

Institutional Source

Beutler Lab

Gene Symbol

Arid1a

Ensembl Gene

ENSMUSG00000007880

Gene Name

AT-rich interaction domain 1A

Synonyms

Smarcf1, 1110030E03Rik, Osa1, BAF250a

MMRRC Submission

041783-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4552 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

133406319-133484080 bp(-) (GRCm39)

Type of Mutation

intron

DNA Base Change (assembly)

A to C at 133423010 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000122354 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000008024] [ENSMUST00000105897] [ENSMUST00000145664]

AlphaFold

A2BH40

Predicted Effect

probably benign
Transcript: ENSMUST00000008024

SMART Domains

Protein: ENSMUSP00000008024
Gene: ENSMUSG00000007880

Domain	Start	End	E-Value	Type
low complexity region	17	42	N/A	INTRINSIC
low complexity region	86	110	N/A	INTRINSIC
low complexity region	113	211	N/A	INTRINSIC
low complexity region	226	237	N/A	INTRINSIC
low complexity region	274	290	N/A	INTRINSIC
low complexity region	310	323	N/A	INTRINSIC
internal_repeat_3	329	402	4.13e-5	PROSPERO
low complexity region	410	426	N/A	INTRINSIC
low complexity region	429	442	N/A	INTRINSIC
internal_repeat_1	443	563	4.59e-6	PROSPERO
internal_repeat_2	461	595	1.38e-5	PROSPERO
low complexity region	604	626	N/A	INTRINSIC
ARID	630	720	3.56e-25	SMART
BRIGHT	634	725	3.76e-31	SMART
low complexity region	739	751	N/A	INTRINSIC
low complexity region	756	770	N/A	INTRINSIC
internal_repeat_3	778	872	4.13e-5	PROSPERO
internal_repeat_2	781	928	1.38e-5	PROSPERO
internal_repeat_1	825	940	4.59e-6	PROSPERO
low complexity region	962	987	N/A	INTRINSIC
low complexity region	1014	1045	N/A	INTRINSIC
low complexity region	1187	1200	N/A	INTRINSIC
low complexity region	1380	1404	N/A	INTRINSIC
low complexity region	1500	1518	N/A	INTRINSIC
Pfam:DUF3518	1592	1848	1.8e-146	PFAM
low complexity region	1849	1859	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000105897

SMART Domains

Protein: ENSMUSP00000101517
Gene: ENSMUSG00000007880

Domain	Start	End	E-Value	Type
low complexity region	2	10	N/A	INTRINSIC
low complexity region	24	52	N/A	INTRINSIC
low complexity region	74	96	N/A	INTRINSIC
low complexity region	118	148	N/A	INTRINSIC
low complexity region	161	169	N/A	INTRINSIC
low complexity region	233	266	N/A	INTRINSIC
low complexity region	273	295	N/A	INTRINSIC
low complexity region	308	332	N/A	INTRINSIC
low complexity region	367	373	N/A	INTRINSIC
low complexity region	402	427	N/A	INTRINSIC
low complexity region	471	495	N/A	INTRINSIC
low complexity region	498	596	N/A	INTRINSIC
low complexity region	611	622	N/A	INTRINSIC
low complexity region	659	675	N/A	INTRINSIC
low complexity region	695	708	N/A	INTRINSIC
low complexity region	795	811	N/A	INTRINSIC
low complexity region	814	827	N/A	INTRINSIC
internal_repeat_2	828	948	9.26e-7	PROSPERO
internal_repeat_1	831	980	9.26e-7	PROSPERO
low complexity region	989	1011	N/A	INTRINSIC
ARID	1015	1105	3.56e-25	SMART
BRIGHT	1019	1110	3.76e-31	SMART
low complexity region	1124	1136	N/A	INTRINSIC
low complexity region	1141	1155	N/A	INTRINSIC
internal_repeat_1	1159	1314	9.26e-7	PROSPERO
internal_repeat_2	1211	1326	9.26e-7	PROSPERO
low complexity region	1343	1368	N/A	INTRINSIC
low complexity region	1395	1426	N/A	INTRINSIC
low complexity region	1568	1581	N/A	INTRINSIC
low complexity region	1761	1785	N/A	INTRINSIC
low complexity region	1881	1899	N/A	INTRINSIC
Pfam:DUF3518	1973	2229	1.4e-146	PFAM
low complexity region	2230	2240	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138473

Predicted Effect

probably benign
Transcript: ENSMUST00000145664

SMART Domains

Protein: ENSMUSP00000122354
Gene: ENSMUSG00000007880

Domain	Start	End	E-Value	Type
low complexity region	2	10	N/A	INTRINSIC
low complexity region	24	52	N/A	INTRINSIC
low complexity region	74	96	N/A	INTRINSIC
low complexity region	118	148	N/A	INTRINSIC
low complexity region	161	169	N/A	INTRINSIC
low complexity region	233	266	N/A	INTRINSIC
low complexity region	273	295	N/A	INTRINSIC
low complexity region	308	332	N/A	INTRINSIC
low complexity region	367	373	N/A	INTRINSIC
low complexity region	402	427	N/A	INTRINSIC
low complexity region	471	495	N/A	INTRINSIC
low complexity region	498	596	N/A	INTRINSIC
low complexity region	611	622	N/A	INTRINSIC
low complexity region	659	675	N/A	INTRINSIC
low complexity region	695	708	N/A	INTRINSIC
internal_repeat_3	714	787	9.49e-6	PROSPERO
low complexity region	795	811	N/A	INTRINSIC
low complexity region	814	827	N/A	INTRINSIC
internal_repeat_1	828	948	8.73e-7	PROSPERO
internal_repeat_2	846	980	2.88e-6	PROSPERO
low complexity region	989	1011	N/A	INTRINSIC
ARID	1015	1105	3.56e-25	SMART
BRIGHT	1019	1110	3.76e-31	SMART
low complexity region	1124	1136	N/A	INTRINSIC
low complexity region	1141	1155	N/A	INTRINSIC
internal_repeat_3	1163	1257	9.49e-6	PROSPERO
internal_repeat_2	1166	1313	2.88e-6	PROSPERO
internal_repeat_1	1210	1325	8.73e-7	PROSPERO
low complexity region	1347	1372	N/A	INTRINSIC
low complexity region	1399	1430	N/A	INTRINSIC
low complexity region	1572	1585	N/A	INTRINSIC
low complexity region	1765	1789	N/A	INTRINSIC
low complexity region	1885	1903	N/A	INTRINSIC
Pfam:DUF3518	1978	2233	1.3e-117	PFAM
low complexity region	2234	2244	N/A	INTRINSIC

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.9%
20x: 94.4%

Validation Efficiency

97% (62/64)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the SWI/SNF family, whose members 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. It possesses at least two conserved domains that could be important for its function. First, it has a DNA-binding domain that can specifically bind an AT-rich DNA sequence known to be recognized by a SNF/SWI complex at the beta-globin locus. Second, the C-terminus of the protein can stimulate glucocorticoid receptor-dependent transcriptional activation. It is thought that the protein encoded by this gene confers specificity to the SNF/SWI complex and may recruit the complex to its targets through either protein-DNA or protein-protein interactions. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Embryos with homozygous null alleles arrest development at E6.5 with failure to form a mesoderm layer. Mice homozygous for an allele lacking exon 2 and 3 die shortly after birth and exhibit an increase in the hematopoietic stem cell population of the fetal liver at E14.5. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts16	G	A	13: 70,927,637 (GRCm39)		probably benign	Het
Arhgap33	A	T	7: 30,218,533 (GRCm39)		probably benign	Het
C4bp	A	G	1: 130,564,464 (GRCm39)	Y407H	possibly damaging	Het
Camta1	T	C	4: 151,876,959 (GRCm39)	R79G	probably damaging	Het
Caskin1	G	A	17: 24,725,602 (GRCm39)	S1296N	probably benign	Het
Cep128	T	C	12: 91,260,936 (GRCm39)	E309G	probably damaging	Het
Chit1	A	G	1: 134,071,789 (GRCm39)	T100A	probably benign	Het
Dalrd3	A	G	9: 108,449,429 (GRCm39)	D454G	possibly damaging	Het
Ddx19a	G	A	8: 111,705,198 (GRCm39)	Q308*	probably null	Het
Dmxl2	T	C	9: 54,359,047 (GRCm39)	N395S	probably damaging	Het
Dnah17	T	C	11: 117,943,769 (GRCm39)	D3125G	possibly damaging	Het
Dnah5	T	C	15: 28,397,300 (GRCm39)	V3331A	probably benign	Het
Dnah9	T	C	11: 65,732,192 (GRCm39)	E4238G	probably damaging	Het
Dner	T	C	1: 84,361,578 (GRCm39)	Y677C	probably damaging	Het
Epgn	A	T	5: 91,175,421 (GRCm39)	K14*	probably null	Het
Hid1	G	A	11: 115,249,505 (GRCm39)	T240M	possibly damaging	Het
Igbp1b	T	A	6: 138,635,112 (GRCm39)	M111L	probably benign	Het
Kif26b	T	A	1: 178,711,600 (GRCm39)	I740N	probably damaging	Het
Klk4	C	A	7: 43,533,443 (GRCm39)	H101N	probably benign	Het
Mrgpra2b	C	A	7: 47,113,754 (GRCm39)	S300I	probably benign	Het
Mtss2	A	G	8: 111,465,137 (GRCm39)	T464A	probably damaging	Het
Nbas	T	C	12: 13,385,938 (GRCm39)		probably null	Het
Nif3l1	C	T	1: 58,488,483 (GRCm39)		probably benign	Het
Noct	T	A	3: 51,157,589 (GRCm39)	I309N	probably benign	Het
Obscn	T	C	11: 59,022,472 (GRCm39)	R758G	possibly damaging	Het
Odf2l	A	T	3: 144,856,844 (GRCm39)	T600S	probably benign	Het
Odf4	C	T	11: 68,812,866 (GRCm39)	S264N	probably benign	Het
Or13a17	A	T	7: 140,271,655 (GRCm39)	Y279F	probably damaging	Het
Or1m1	A	G	9: 18,666,430 (GRCm39)	V167A	possibly damaging	Het
Or2y1e	A	T	11: 49,218,777 (GRCm39)	M180L	probably benign	Het
Or6c217	T	C	10: 129,737,992 (GRCm39)	M196V	probably benign	Het
Papolb	T	C	5: 142,514,933 (GRCm39)	I237V	probably benign	Het
Parpbp	T	A	10: 87,929,564 (GRCm39)	Q428L	possibly damaging	Het
Pclo	T	C	5: 14,719,285 (GRCm39)	S1141P	unknown	Het
Plcb1	T	C	2: 135,177,413 (GRCm39)	S582P	probably benign	Het
Ppargc1a	C	T	5: 51,620,557 (GRCm39)		probably benign	Het
Ptchd4	A	T	17: 42,813,346 (GRCm39)	I416L	probably benign	Het
Rhpn1	G	A	15: 75,585,968 (GRCm39)	R627H	probably benign	Het
Ric8a	G	A	7: 140,441,250 (GRCm39)	G182S	probably damaging	Het
Rims1	T	C	1: 22,443,718 (GRCm39)	D895G	probably damaging	Het
Rrp1b	G	A	17: 32,274,984 (GRCm39)		probably benign	Het
Rtf1	T	A	2: 119,561,210 (GRCm39)	D636E	probably benign	Het
Scn3a	T	C	2: 65,354,523 (GRCm39)	D333G	probably benign	Het
Sema6a	A	G	18: 47,424,990 (GRCm39)	L207P	probably damaging	Het
Shcbp1	A	T	8: 4,799,779 (GRCm39)	Y160*	probably null	Het
Slc27a1	A	T	8: 72,032,710 (GRCm39)		probably null	Het
Ston2	C	T	12: 91,608,646 (GRCm39)	R818Q	probably damaging	Het
Tipin	T	A	9: 64,195,385 (GRCm39)		probably null	Het
Tjap1	A	T	17: 46,570,953 (GRCm39)		probably null	Het
Vmn1r117	A	T	7: 20,617,517 (GRCm39)	F177Y	probably damaging	Het
Vmn1r57	A	G	7: 5,223,667 (GRCm39)	D64G	possibly damaging	Het
Vmn2r73	T	A	7: 85,525,055 (GRCm39)	D31V	probably benign	Het
Vmn2r-ps41	A	T	7: 9,180,063 (GRCm39)		noncoding transcript	Het

Other mutations in Arid1a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00565:Arid1a	APN	4	133,412,793 (GRCm39)	missense	unknown
IGL01139:Arid1a	APN	4	133,421,308 (GRCm39)	missense	unknown
IGL01392:Arid1a	APN	4	133,408,348 (GRCm39)	missense	unknown
IGL01543:Arid1a	APN	4	133,409,033 (GRCm39)	missense	unknown
IGL01642:Arid1a	APN	4	133,409,155 (GRCm39)	missense	unknown
IGL01843:Arid1a	APN	4	133,408,765 (GRCm39)	missense	unknown
IGL02108:Arid1a	APN	4	133,407,827 (GRCm39)	missense	unknown
IGL02117:Arid1a	APN	4	133,420,126 (GRCm39)	missense	unknown
IGL02150:Arid1a	APN	4	133,414,568 (GRCm39)	missense	unknown
IGL02478:Arid1a	APN	4	133,408,585 (GRCm39)	missense	unknown
IGL02544:Arid1a	APN	4	133,409,059 (GRCm39)	missense	unknown
IGL03070:Arid1a	APN	4	133,422,064 (GRCm39)	missense	unknown
PIT4520001:Arid1a	UTSW	4	133,409,227 (GRCm39)	missense	unknown
R0023:Arid1a	UTSW	4	133,418,487 (GRCm39)	missense	unknown
R0023:Arid1a	UTSW	4	133,418,487 (GRCm39)	missense	unknown
R0419:Arid1a	UTSW	4	133,408,435 (GRCm39)	missense	unknown
R0452:Arid1a	UTSW	4	133,416,416 (GRCm39)	missense	unknown
R0631:Arid1a	UTSW	4	133,416,481 (GRCm39)	missense	unknown
R0648:Arid1a	UTSW	4	133,412,515 (GRCm39)	missense	unknown
R1004:Arid1a	UTSW	4	133,414,586 (GRCm39)	missense	unknown
R1225:Arid1a	UTSW	4	133,414,676 (GRCm39)	missense	unknown
R1229:Arid1a	UTSW	4	133,418,548 (GRCm39)	missense	unknown
R1435:Arid1a	UTSW	4	133,408,009 (GRCm39)	missense	unknown
R1480:Arid1a	UTSW	4	133,407,700 (GRCm39)	missense	unknown
R1491:Arid1a	UTSW	4	133,448,237 (GRCm39)	missense	unknown
R1674:Arid1a	UTSW	4	133,416,571 (GRCm39)	missense	unknown
R1909:Arid1a	UTSW	4	133,421,072 (GRCm39)	missense	unknown
R1960:Arid1a	UTSW	4	133,480,401 (GRCm39)	missense	possibly damaging	0.84
R2018:Arid1a	UTSW	4	133,409,145 (GRCm39)	missense	unknown
R2147:Arid1a	UTSW	4	133,408,677 (GRCm39)	missense	unknown
R2303:Arid1a	UTSW	4	133,414,562 (GRCm39)	missense	unknown
R2320:Arid1a	UTSW	4	133,407,840 (GRCm39)	missense	unknown
R3775:Arid1a	UTSW	4	133,414,075 (GRCm39)	missense	unknown
R3907:Arid1a	UTSW	4	133,420,223 (GRCm39)	splice site	probably benign
R4509:Arid1a	UTSW	4	133,423,010 (GRCm39)	intron	probably benign
R4510:Arid1a	UTSW	4	133,423,010 (GRCm39)	intron	probably benign
R4551:Arid1a	UTSW	4	133,423,010 (GRCm39)	intron	probably benign
R4606:Arid1a	UTSW	4	133,414,634 (GRCm39)	missense	unknown
R4745:Arid1a	UTSW	4	133,480,417 (GRCm39)	missense	probably benign	0.33
R4851:Arid1a	UTSW	4	133,408,672 (GRCm39)	missense	unknown
R4867:Arid1a	UTSW	4	133,448,168 (GRCm39)	missense	probably benign	0.01
R5203:Arid1a	UTSW	4	133,409,314 (GRCm39)	missense	unknown
R5227:Arid1a	UTSW	4	133,407,716 (GRCm39)	missense	unknown
R5294:Arid1a	UTSW	4	133,418,366 (GRCm39)	splice site	probably benign
R5299:Arid1a	UTSW	4	133,414,537 (GRCm39)	missense	unknown
R5412:Arid1a	UTSW	4	133,446,913 (GRCm39)	unclassified	probably benign
R5540:Arid1a	UTSW	4	133,407,765 (GRCm39)	missense	unknown
R5704:Arid1a	UTSW	4	133,409,050 (GRCm39)	missense	unknown
R5870:Arid1a	UTSW	4	133,408,387 (GRCm39)	missense	unknown
R6092:Arid1a	UTSW	4	133,421,163 (GRCm39)	missense	unknown
R6151:Arid1a	UTSW	4	133,412,287 (GRCm39)	missense	unknown
R6240:Arid1a	UTSW	4	133,407,997 (GRCm39)	missense	unknown
R6379:Arid1a	UTSW	4	133,408,238 (GRCm39)	missense	unknown
R6427:Arid1a	UTSW	4	133,408,835 (GRCm39)	missense	unknown
R6739:Arid1a	UTSW	4	133,414,937 (GRCm39)	missense	unknown
R7159:Arid1a	UTSW	4	133,480,879 (GRCm39)	missense	unknown
R7186:Arid1a	UTSW	4	133,480,544 (GRCm39)
R7354:Arid1a	UTSW	4	133,421,258 (GRCm39)	missense	unknown
R7408:Arid1a	UTSW	4	133,408,391 (GRCm39)	missense	unknown
R7452:Arid1a	UTSW	4	133,480,438 (GRCm39)	missense	possibly damaging	0.86
R7471:Arid1a	UTSW	4	133,408,355 (GRCm39)	missense	unknown
R7478:Arid1a	UTSW	4	133,412,482 (GRCm39)	missense	unknown
R7581:Arid1a	UTSW	4	133,407,662 (GRCm39)	missense	unknown
R7614:Arid1a	UTSW	4	133,418,466 (GRCm39)	missense	unknown
R7712:Arid1a	UTSW	4	133,479,922 (GRCm39)	missense	probably benign	0.14
R7734:Arid1a	UTSW	4	133,408,679 (GRCm39)	missense	unknown
R7878:Arid1a	UTSW	4	133,414,582 (GRCm39)	missense	unknown
R7973:Arid1a	UTSW	4	133,480,381 (GRCm39)	missense	probably damaging	0.96
R8012:Arid1a	UTSW	4	133,420,174 (GRCm39)	missense	unknown
R8355:Arid1a	UTSW	4	133,448,174 (GRCm39)	missense	unknown
R8396:Arid1a	UTSW	4	133,479,973 (GRCm39)	missense	probably damaging	0.99
R8708:Arid1a	UTSW	4	133,409,145 (GRCm39)	missense	unknown
R8923:Arid1a	UTSW	4	133,412,304 (GRCm39)	missense	unknown
R8997:Arid1a	UTSW	4	133,421,343 (GRCm39)	missense	unknown
R9003:Arid1a	UTSW	4	133,411,799 (GRCm39)	missense	unknown
R9145:Arid1a	UTSW	4	133,421,214 (GRCm39)	missense	unknown
R9224:Arid1a	UTSW	4	133,409,167 (GRCm39)	missense	unknown
R9310:Arid1a	UTSW	4	133,413,625 (GRCm39)	missense	unknown
R9470:Arid1a	UTSW	4	133,413,057 (GRCm39)	missense	unknown
RF012:Arid1a	UTSW	4	133,480,131 (GRCm39)	small deletion	probably benign
RF015:Arid1a	UTSW	4	133,480,142 (GRCm39)	small deletion	probably benign
X0064:Arid1a	UTSW	4	133,416,571 (GRCm39)	missense	unknown
Z1176:Arid1a	UTSW	4	133,447,861 (GRCm39)	missense	probably null
Z1177:Arid1a	UTSW	4	133,408,227 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- GACTTTGGCCCAGCATGTTTG -3'
(R):5'- TTTGACTCGTGCCTGCATGG -3'

Sequencing Primer
(F):5'- CATGTCACAATAGTGGTAGATTGG -3'
(R):5'- CATGGTTTTTCCCTTAGCATTTGAAG -3'

Posted On

2016-04-06