Mutagenetix > Incidental Mutation

Incidental Mutation 'R3870:Satb2'

276478

Institutional Source

Beutler Lab

Gene Symbol

Satb2

Ensembl Gene

ENSMUSG00000038331

Gene Name

special AT-rich sequence binding protein 2

Synonyms

BAP002

MMRRC Submission

040789-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3870 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

56833140-57017809 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 56930379 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 215 (S215P)

Ref Sequence

ENSEMBL: ENSMUSP00000110057 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000042857] [ENSMUST00000114415] [ENSMUST00000177424]

AlphaFold

Q8VI24

Predicted Effect

probably damaging
Transcript: ENSMUST00000042857
AA Change: S156P

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

SMART Domains

Protein: ENSMUSP00000046067
Gene: ENSMUSG00000038331
AA Change: S156P

Domain	Start	End	E-Value	Type
PDB:3TUO\|D	45	98	8e-19	PDB
PDB:3NZL\|A	106	174	4e-35	PDB
low complexity region	235	251	N/A	INTRINSIC
CUT	292	378	1.3e-36	SMART
low complexity region	381	399	N/A	INTRINSIC
CUT	415	501	3.58e-39	SMART
low complexity region	510	524	N/A	INTRINSIC
low complexity region	533	551	N/A	INTRINSIC
HOX	555	618	1.06e-7	SMART
low complexity region	629	650	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000114415
AA Change: S215P

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

SMART Domains

Protein: ENSMUSP00000110057
Gene: ENSMUSG00000038331
AA Change: S215P

Domain	Start	End	E-Value	Type
Pfam:ULD	58	156	1.7e-39	PFAM
Pfam:CUTL	162	233	3.9e-46	PFAM
low complexity region	294	310	N/A	INTRINSIC
CUT	351	437	1.3e-36	SMART
low complexity region	440	458	N/A	INTRINSIC
CUT	474	560	3.58e-39	SMART
low complexity region	569	583	N/A	INTRINSIC
low complexity region	592	610	N/A	INTRINSIC
HOX	614	677	1.06e-7	SMART
low complexity region	688	709	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000177424

SMART Domains

Protein: ENSMUSP00000135391
Gene: ENSMUSG00000038331

Domain	Start	End	E-Value	Type
PDB:3TUO\|D	57	115	6e-23	PDB
low complexity region	176	192	N/A	INTRINSIC
CUT	233	319	1.3e-36	SMART
low complexity region	322	340	N/A	INTRINSIC
CUT	356	442	3.58e-39	SMART
low complexity region	451	465	N/A	INTRINSIC
low complexity region	474	492	N/A	INTRINSIC
HOX	496	559	1.06e-7	SMART
low complexity region	570	591	N/A	INTRINSIC

Meta Mutation Damage Score

0.2150

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.6%
20x: 96.1%

Validation Efficiency

90% (61/68)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a DNA binding protein that specifically binds nuclear matrix attachment regions. The encoded protein is involved in transcription regulation and chromatin remodeling. Defects in this gene are associated with isolated cleft palate and mental retardation. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Feb 2010]
PHENOTYPE: Homozygous inactivation of this gene causes complete perinatal lethality and craniofacial anomalies, such as cleft palate, micrognathia, microcephaly, decreased tongue size, absent incisors and nasal capsule hypoplasia, and leads to short limbs and defects in osteoblast differentiation and function. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700028J19Rik	T	A	7: 43,880,828 (GRCm39)		probably null	Het
Adam22	C	A	5: 8,182,418 (GRCm39)	C514F	probably damaging	Het
Akap8	G	A	17: 32,536,813 (GRCm39)		probably benign	Het
Armcx2	A	T	X: 133,707,048 (GRCm39)	V195E	probably benign	Het
Atg7	T	C	6: 114,674,008 (GRCm39)	S301P	possibly damaging	Het
Cc2d2a	C	A	5: 43,876,033 (GRCm39)	Y1003*	probably null	Het
Ccdc93	A	G	1: 121,390,843 (GRCm39)	S272G	probably benign	Het
Ces1d	C	G	8: 93,901,714 (GRCm39)	L418F	probably benign	Het
Cntnap5a	A	G	1: 115,987,979 (GRCm39)	E170G	probably damaging	Het
Cplane1	A	T	15: 8,247,948 (GRCm39)	K1499M	probably damaging	Het
Crygs	C	T	16: 22,624,301 (GRCm39)	G102D	possibly damaging	Het
Ehd4	T	A	2: 119,967,434 (GRCm39)	D120V	probably damaging	Het
Eif4g3	T	A	4: 137,824,211 (GRCm39)	V71E	probably damaging	Het
Exoc5	A	G	14: 49,256,853 (GRCm39)		probably benign	Het
Glud1	T	A	14: 34,047,537 (GRCm39)		probably benign	Het
Gm10985	TTCTCTCTCTCTCTCTCT	TTCTCTCTCTCTCTCT	3: 53,752,626 (GRCm39)		probably null	Het
Gm11555	G	T	11: 99,540,816 (GRCm39)	C64*	probably null	Het
Gm5468	A	G	15: 25,414,561 (GRCm39)		probably benign	Het
Gpatch2	T	A	1: 187,054,491 (GRCm39)	L74Q	probably damaging	Het
Hnrnpa0	G	A	13: 58,275,713 (GRCm39)	R139C	probably damaging	Het
Hrh1	A	G	6: 114,457,880 (GRCm39)	Y387C	probably damaging	Het
Ldb3	A	T	14: 34,289,440 (GRCm39)	D216E	probably damaging	Het
Lingo1	A	T	9: 56,527,009 (GRCm39)	S533T	probably benign	Het
Lmtk2	T	G	5: 144,103,245 (GRCm39)		probably benign	Het
Map1s	A	G	8: 71,369,745 (GRCm39)	E939G	possibly damaging	Het
Mast1	G	A	8: 85,645,360 (GRCm39)	T695I	probably damaging	Het
Mettl21e	G	A	1: 44,245,524 (GRCm39)	R241W	probably benign	Het
Mfsd4a	G	A	1: 131,974,091 (GRCm39)	T261I	probably damaging	Het
Mmel1	T	C	4: 154,968,095 (GRCm39)	S144P	probably benign	Het
Myo16	A	T	8: 10,492,239 (GRCm39)	H727L	probably benign	Het
Ncoa6	T	C	2: 155,257,477 (GRCm39)		probably null	Het
Nipa2	T	C	7: 55,582,690 (GRCm39)	R352G	probably damaging	Het
Oaf	C	T	9: 43,134,055 (GRCm39)	R222Q	probably benign	Het
Or2ag2b	T	A	7: 106,418,047 (GRCm39)	Y252*	probably null	Het
Pard3	T	C	8: 128,136,167 (GRCm39)	S847P	probably damaging	Het
Pgbd1	C	T	13: 21,618,540 (GRCm39)	R39H	possibly damaging	Het
Plcb1	A	C	2: 135,167,591 (GRCm39)	I462L	probably damaging	Het
Prex2	T	C	1: 11,230,416 (GRCm39)	V814A	possibly damaging	Het
Rasal3	G	A	17: 32,612,522 (GRCm39)	R780W	possibly damaging	Het
Rubcnl	C	T	14: 75,278,356 (GRCm39)	P380L	probably benign	Het
Ryk	A	G	9: 102,768,427 (GRCm39)	E359G	probably damaging	Het
Sall2	C	A	14: 52,551,451 (GRCm39)	L579F	probably damaging	Het
Scg3	T	C	9: 75,582,781 (GRCm39)		probably benign	Het
Slc35f5	A	G	1: 125,490,098 (GRCm39)	T65A	probably benign	Het
Snx33	T	C	9: 56,834,024 (GRCm39)	N15S	probably benign	Het
Stat2	T	A	10: 128,113,762 (GRCm39)	S180R	probably benign	Het
Stxbp2	A	G	8: 3,684,079 (GRCm39)	T129A	probably damaging	Het
Tas1r3	A	T	4: 155,945,810 (GRCm39)	C529S	probably damaging	Het
Tlr12	T	A	4: 128,510,361 (GRCm39)	M630L	probably benign	Het
Tnfrsf10b	T	G	14: 70,010,905 (GRCm39)	D103E	probably benign	Het
Togaram1	A	C	12: 65,049,419 (GRCm39)	E1285D	probably benign	Het
Tppp	A	G	13: 74,178,891 (GRCm39)	T111A	probably benign	Het
Trim12c	T	C	7: 103,997,544 (GRCm39)	Q4R	probably benign	Het
Ttbk2	T	G	2: 120,570,500 (GRCm39)	S1149R	probably damaging	Het
Uncx	T	C	5: 139,533,120 (GRCm39)	L395P	probably damaging	Het
Usp14	A	G	18: 10,002,370 (GRCm39)	S314P	possibly damaging	Het
Usp32	A	T	11: 84,897,881 (GRCm39)	Y1153*	probably null	Het
Vmn2r6	T	C	3: 64,464,042 (GRCm39)	E264G	probably damaging	Het
Vmn2r77	T	C	7: 86,461,050 (GRCm39)	F792S	probably damaging	Het
Vps13c	A	G	9: 67,792,008 (GRCm39)	I425V	probably benign	Het
Vstm4	C	T	14: 32,585,712 (GRCm39)	A93V	probably benign	Het
Xrcc6	T	A	15: 81,909,885 (GRCm39)	S97T	probably benign	Het
Zscan20	A	G	4: 128,480,218 (GRCm39)	C758R	probably damaging	Het

Other mutations in Satb2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00742:Satb2	APN	1	56,870,700 (GRCm39)	missense	possibly damaging	0.56
IGL02008:Satb2	APN	1	56,835,952 (GRCm39)	missense	possibly damaging	0.70
IGL02209:Satb2	APN	1	56,910,677 (GRCm39)	missense	probably damaging	1.00
IGL02956:Satb2	APN	1	56,987,334 (GRCm39)	missense	probably damaging	0.99
IGL03214:Satb2	APN	1	56,884,739 (GRCm39)	missense	probably damaging	1.00
IGL03272:Satb2	APN	1	56,884,802 (GRCm39)	missense	probably damaging	1.00
IGL03356:Satb2	APN	1	56,930,333 (GRCm39)	missense	probably damaging	1.00
Optimism	UTSW	1	56,884,880 (GRCm39)	nonsense	probably null
prophecy	UTSW	1	56,884,778 (GRCm39)	missense	probably damaging	1.00
R0990:Satb2	UTSW	1	56,889,343 (GRCm39)	missense	probably damaging	0.96
R1534:Satb2	UTSW	1	56,987,392 (GRCm39)	nonsense	probably null
R1711:Satb2	UTSW	1	56,889,448 (GRCm39)	missense	probably damaging	0.99
R1952:Satb2	UTSW	1	56,938,229 (GRCm39)	missense	probably damaging	1.00
R2404:Satb2	UTSW	1	56,987,267 (GRCm39)	missense	probably damaging	1.00
R3792:Satb2	UTSW	1	56,884,779 (GRCm39)	missense	probably damaging	1.00
R3871:Satb2	UTSW	1	56,930,379 (GRCm39)	missense	probably damaging	1.00
R4333:Satb2	UTSW	1	56,884,745 (GRCm39)	missense	probably damaging	1.00
R4621:Satb2	UTSW	1	56,884,778 (GRCm39)	missense	probably damaging	1.00
R4962:Satb2	UTSW	1	56,930,327 (GRCm39)	missense	probably benign	0.25
R5296:Satb2	UTSW	1	56,836,066 (GRCm39)	missense	probably damaging	0.99
R5314:Satb2	UTSW	1	56,870,686 (GRCm39)	missense	probably damaging	0.99
R5407:Satb2	UTSW	1	56,987,309 (GRCm39)	missense	probably damaging	1.00
R5925:Satb2	UTSW	1	56,836,097 (GRCm39)	missense	possibly damaging	0.80
R6355:Satb2	UTSW	1	56,987,356 (GRCm39)	missense	probably damaging	1.00
R6634:Satb2	UTSW	1	56,884,880 (GRCm39)	nonsense	probably null
R6645:Satb2	UTSW	1	56,836,166 (GRCm39)	missense	possibly damaging	0.51
R7578:Satb2	UTSW	1	56,910,943 (GRCm39)	missense	probably benign	0.01
R7694:Satb2	UTSW	1	56,910,683 (GRCm39)	missense	probably benign
R7811:Satb2	UTSW	1	56,884,880 (GRCm39)	missense	probably benign	0.19
R7961:Satb2	UTSW	1	56,910,917 (GRCm39)	missense	probably benign	0.01
R8009:Satb2	UTSW	1	56,910,917 (GRCm39)	missense	probably benign	0.01
R8023:Satb2	UTSW	1	56,930,390 (GRCm39)	missense	probably damaging	1.00
R8094:Satb2	UTSW	1	56,870,623 (GRCm39)	missense	possibly damaging	0.95
R8745:Satb2	UTSW	1	57,008,796 (GRCm39)	missense	unknown
R8960:Satb2	UTSW	1	56,910,470 (GRCm39)	critical splice donor site	probably null
R9382:Satb2	UTSW	1	56,870,797 (GRCm39)	critical splice acceptor site	probably null

Predicted Primers

PCR Primer
(F):5'- GATGCGTCAGTGCTCATTCC -3'
(R):5'- CGTTTGTAGAGGAGTCATAGCTTTAAG -3'

Sequencing Primer
(F):5'- GTGCTCATTCCAACTTGTTAATCAG -3'
(R):5'- GTCTCTTCTGGTCGCTAA -3'

Posted On

2015-04-06