Mutagenetix > Incidental Mutation

Incidental Mutation 'R5652:Satb1'

441532

Institutional Source

Beutler Lab

Gene Symbol

Satb1

Ensembl Gene

ENSMUSG00000023927

Gene Name

special AT-rich sequence binding protein 1

Synonyms

2610306G12Rik

MMRRC Submission

043298-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5652 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

52043215-52140318 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 52049823 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 544 (T544S)

Ref Sequence

ENSEMBL: ENSMUSP00000134957 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000129667] [ENSMUST00000133574] [ENSMUST00000140979] [ENSMUST00000144331] [ENSMUST00000152830] [ENSMUST00000169480] [ENSMUST00000176669]

AlphaFold

Q60611

Predicted Effect

probably damaging
Transcript: ENSMUST00000129667
AA Change: T544S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000116020
Gene: ENSMUSG00000023927
AA Change: T544S

Domain	Start	End	E-Value	Type
PDB:3TUO\|D	71	171	5e-66	PDB
PDB:3NZL\|A	179	250	5e-45	PDB
Blast:CUT	245	327	9e-48	BLAST
CUT	362	448	1.08e-38	SMART
CUT	485	571	4.41e-39	SMART
low complexity region	593	619	N/A	INTRINSIC
HOX	644	707	6.73e-10	SMART
low complexity region	720	730	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000133574
AA Change: T544S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000120536
Gene: ENSMUSG00000023927
AA Change: T544S

Domain	Start	End	E-Value	Type
PDB:3TUO\|D	71	171	5e-66	PDB
PDB:3NZL\|A	179	250	5e-45	PDB
Blast:CUT	245	327	9e-48	BLAST
CUT	362	448	1.08e-38	SMART
CUT	485	571	4.41e-39	SMART
low complexity region	593	620	N/A	INTRINSIC
HOX	645	708	6.73e-10	SMART
low complexity region	721	731	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137697

Predicted Effect

possibly damaging
Transcript: ENSMUST00000140979
AA Change: T544S

PolyPhen 2 Score 0.822 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000118839
Gene: ENSMUSG00000023927
AA Change: T544S

Domain	Start	End	E-Value	Type
Pfam:ULD	72	170	3.2e-40	PFAM
Pfam:CUTL	176	247	1.6e-46	PFAM
CUT	362	448	1.08e-38	SMART
CUT	485	571	4.41e-39	SMART
low complexity region	616	661	N/A	INTRINSIC
HOX	676	739	6.73e-10	SMART
low complexity region	752	762	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000144331
AA Change: T544S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000116006
Gene: ENSMUSG00000023927
AA Change: T544S

Domain	Start	End	E-Value	Type
PDB:3TUO\|D	71	171	5e-66	PDB
PDB:3NZL\|A	179	250	5e-45	PDB
Blast:CUT	245	327	9e-48	BLAST
CUT	362	448	1.08e-38	SMART
CUT	485	571	4.41e-39	SMART
low complexity region	593	620	N/A	INTRINSIC
HOX	645	708	6.73e-10	SMART
low complexity region	721	731	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000152830
AA Change: T544S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000119842
Gene: ENSMUSG00000023927
AA Change: T544S

Domain	Start	End	E-Value	Type
PDB:3TUO\|D	71	171	5e-66	PDB
PDB:3NZL\|A	179	250	5e-45	PDB
Blast:CUT	245	327	9e-48	BLAST
CUT	362	448	1.08e-38	SMART
CUT	485	571	4.41e-39	SMART
low complexity region	593	620	N/A	INTRINSIC
HOX	645	708	6.73e-10	SMART
low complexity region	721	731	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000169480
AA Change: T544S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000128841
Gene: ENSMUSG00000023927
AA Change: T544S

Domain	Start	End	E-Value	Type
PDB:3TUO\|D	71	171	5e-66	PDB
PDB:3NZL\|A	179	250	5e-45	PDB
Blast:CUT	245	327	9e-48	BLAST
CUT	362	448	1.08e-38	SMART
CUT	485	571	4.41e-39	SMART
low complexity region	593	620	N/A	INTRINSIC
HOX	645	708	6.73e-10	SMART
low complexity region	721	731	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000176669
AA Change: T544S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000134957
Gene: ENSMUSG00000023927
AA Change: T544S

Domain	Start	End	E-Value	Type
PDB:3TUO\|D	71	171	5e-66	PDB
PDB:3NZL\|A	179	250	5e-45	PDB
Blast:CUT	245	327	9e-48	BLAST
CUT	362	448	1.08e-38	SMART
CUT	485	571	4.41e-39	SMART
low complexity region	593	620	N/A	INTRINSIC
HOX	645	708	6.73e-10	SMART
low complexity region	721	731	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000194215

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.2%
20x: 95.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a matrix protein which binds nuclear matrix and scaffold-associating DNAs through a unique nuclear architecture. The protein recruits chromatin-remodeling factors in order to regulate chromatin structure and gene expression. [provided by RefSeq, Apr 2016]
PHENOTYPE: Homozygous mice for a targeted null mutation exhibit reduced size of the lymphoid organs, abnormal T cell development, general growth retardation and die by 3-4 weeks of age. Mice homozegous for a different targeted allele exhibit postnatal growth retardation and postnatal lethality. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc4	T	C	14: 118,856,339 (GRCm39)	I334V	probably benign	Het
Adamts5	C	T	16: 85,696,156 (GRCm39)	A334T	probably damaging	Het
Adcy4	G	C	14: 56,010,900 (GRCm39)	F672L	probably benign	Het
Adgrl1	A	G	8: 84,656,444 (GRCm39)	Y254C	probably damaging	Het
Adnp2	A	G	18: 80,174,065 (GRCm39)	S115P	probably damaging	Het
Aox1	A	T	1: 58,134,356 (GRCm39)	S1110C	probably damaging	Het
Arhgap44	G	T	11: 64,915,064 (GRCm39)	N401K	probably damaging	Het
Atp23	A	T	10: 126,735,494 (GRCm39)	N63K	possibly damaging	Het
Atp8b1	G	C	18: 64,664,453 (GRCm39)	I1238M	probably benign	Het
Ccdc38	A	T	10: 93,391,448 (GRCm39)		probably null	Het
Celsr2	T	C	3: 108,304,051 (GRCm39)	D2364G	probably null	Het
Celsr3	G	A	9: 108,715,671 (GRCm39)	D2116N	probably benign	Het
Cenpf	A	G	1: 189,389,279 (GRCm39)	S1518P	probably damaging	Het
Clcn3	C	A	8: 61,372,387 (GRCm39)	V758L	possibly damaging	Het
Cmklr2	A	G	1: 63,222,626 (GRCm39)	V203A	probably benign	Het
Ctsf	T	C	19: 4,908,505 (GRCm39)	L288P	probably damaging	Het
Cwh43	A	G	5: 73,575,484 (GRCm39)	T334A	probably damaging	Het
Cyp3a57	A	T	5: 145,286,135 (GRCm39)		probably null	Het
Ddr1	C	T	17: 35,997,400 (GRCm39)	A531T	probably benign	Het
Dennd1a	A	G	2: 37,691,138 (GRCm39)	I260T	probably benign	Het
Dgkh	T	C	14: 78,865,201 (GRCm39)	H47R	probably damaging	Het
Dync1h1	G	A	12: 110,632,422 (GRCm39)	V4514I	possibly damaging	Het
Dync2h1	A	T	9: 7,116,638 (GRCm39)	M66K	probably benign	Het
Fam186a	T	G	15: 99,843,253 (GRCm39)	Y997S	possibly damaging	Het
Fam8a1	T	A	13: 46,827,814 (GRCm39)	L334H	probably damaging	Het
Fat4	C	T	3: 39,057,117 (GRCm39)	T4271I	probably damaging	Het
Fdxacb1	T	A	9: 50,679,705 (GRCm39)	L41Q	probably damaging	Het
Fgfr2	C	T	7: 129,863,593 (GRCm39)	V18M	probably damaging	Het
Gpa33	A	C	1: 165,992,714 (GRCm39)		probably null	Het
Gpr107	A	G	2: 31,075,601 (GRCm39)	I371V	probably benign	Het
H1f6	A	G	13: 23,880,219 (GRCm39)	K124R	probably benign	Het
Hectd2	T	C	19: 36,581,720 (GRCm39)	V420A	probably damaging	Het
Iglc3	A	G	16: 18,884,420 (GRCm39)		probably benign	Het
Igtp	A	G	11: 58,097,455 (GRCm39)	T209A	probably benign	Het
Itgb7	T	A	15: 102,124,638 (GRCm39)	N793I	possibly damaging	Het
Kansl1	G	A	11: 104,228,992 (GRCm39)	R870C	probably damaging	Het
Kcnh6	C	T	11: 105,899,811 (GRCm39)	R27C	probably damaging	Het
Kif2b	T	A	11: 91,466,656 (GRCm39)	E542D	possibly damaging	Het
Klhl24	C	A	16: 19,938,997 (GRCm39)	Y517*	probably null	Het
Klhl25	A	G	7: 75,515,895 (GRCm39)	D267G	probably benign	Het
Krr1	C	A	10: 111,813,288 (GRCm39)	F195L	possibly damaging	Het
Lsr	C	T	7: 30,658,456 (GRCm39)	G95D	probably damaging	Het
Matcap2	A	G	9: 22,335,786 (GRCm39)	T135A	probably benign	Het
Med15	A	T	16: 17,473,055 (GRCm39)	I504N	probably damaging	Het
Mug1	A	G	6: 121,817,140 (GRCm39)	R70G	probably benign	Het
Mypn	T	A	10: 62,971,580 (GRCm39)	Q820L	probably damaging	Het
Nlrp4f	A	T	13: 65,330,803 (GRCm39)	H863Q	probably benign	Het
Nudt9	G	A	5: 104,207,646 (GRCm39)	V213M	probably benign	Het
Or5ak4	T	A	2: 85,161,717 (GRCm39)	N175I	probably damaging	Het
Or5k14	A	G	16: 58,692,847 (GRCm39)	L222P	probably damaging	Het
Or7g16	A	G	9: 18,726,922 (GRCm39)	S223P	probably damaging	Het
Or8c13	T	C	9: 38,092,111 (GRCm39)	T3A	probably benign	Het
Orc2	A	G	1: 58,505,231 (GRCm39)	F475L	probably damaging	Het
Oxa1l	T	A	14: 54,604,289 (GRCm39)	L183*	probably null	Het
Pcdh20	T	C	14: 88,704,760 (GRCm39)	T847A	probably damaging	Het
Pcdha6	G	A	18: 37,101,889 (GRCm39)		probably null	Het
Pip5k1a	T	C	3: 94,974,750 (GRCm39)	N376S	probably benign	Het
Pkd1l1	T	C	11: 8,859,889 (GRCm39)	E573G	probably benign	Het
Pkp1	T	A	1: 135,810,335 (GRCm39)		probably null	Het
Pum1	T	C	4: 130,491,438 (GRCm39)	I643T	possibly damaging	Het
Rapgef3	A	G	15: 97,656,318 (GRCm39)	S328P	probably benign	Het
Raver1	A	G	9: 21,001,608 (GRCm39)	V75A	probably damaging	Het
Rbm28	T	C	6: 29,135,408 (GRCm39)	E511G	probably damaging	Het
Sdcbp2	T	C	2: 151,431,135 (GRCm39)	V248A	probably benign	Het
Sema7a	A	G	9: 57,867,942 (GRCm39)	D506G	probably damaging	Het
Septin8	A	G	11: 53,428,044 (GRCm39)	E286G	probably damaging	Het
Sh3pxd2b	A	G	11: 32,372,812 (GRCm39)	I660V	probably damaging	Het
Stk38l	G	T	6: 146,674,826 (GRCm39)	D364Y	possibly damaging	Het
Sycp2	T	C	2: 178,000,498 (GRCm39)		probably null	Het
Tbc1d31	T	A	15: 57,815,062 (GRCm39)	S580T	probably damaging	Het
Tcerg1l	G	A	7: 137,881,775 (GRCm39)	R305C	probably damaging	Het
Tek	T	A	4: 94,743,561 (GRCm39)	Y859N	probably damaging	Het
Tjp1	A	T	7: 64,962,191 (GRCm39)		probably null	Het
Tmem132d	A	T	5: 127,861,859 (GRCm39)	I754N	possibly damaging	Het
Togaram1	G	A	12: 65,063,424 (GRCm39)	V1580I	probably benign	Het
Troap	A	G	15: 98,980,145 (GRCm39)	T442A	probably benign	Het
Ttn	A	T	2: 76,712,097 (GRCm39)		probably benign	Het
Twnk	T	A	19: 44,995,732 (GRCm39)	V55E	possibly damaging	Het
Uggt1	A	T	1: 36,255,234 (GRCm39)	Y225*	probably null	Het
Vmn2r109	A	G	17: 20,760,781 (GRCm39)	*859Q	probably null	Het
Vmn2r17	A	T	5: 109,577,430 (GRCm39)	I494L	probably benign	Het
Vmn2r88	T	C	14: 51,656,029 (GRCm39)	V746A	probably damaging	Het
Yae1d1	A	G	13: 18,166,291 (GRCm39)	L57P	probably damaging	Het
Zfp26	G	A	9: 20,349,137 (GRCm39)	R476*	probably null	Het
Zmynd8	T	A	2: 165,649,618 (GRCm39)	Q816L	probably damaging	Het
Zswim8	A	T	14: 20,763,495 (GRCm39)	H414L	possibly damaging	Het

Other mutations in Satb1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01128:Satb1	APN	17	52,112,317 (GRCm39)	missense	probably damaging	1.00
IGL01658:Satb1	APN	17	52,082,279 (GRCm39)	missense	probably benign	0.33
IGL02070:Satb1	APN	17	52,047,095 (GRCm39)	missense	probably damaging	0.98
IGL02212:Satb1	APN	17	52,082,319 (GRCm39)	missense	possibly damaging	0.82
IGL02971:Satb1	APN	17	52,049,717 (GRCm39)	missense	possibly damaging	0.62
R0049:Satb1	UTSW	17	52,047,374 (GRCm39)	missense	probably benign	0.28
R0056:Satb1	UTSW	17	52,047,231 (GRCm39)	missense	probably damaging	1.00
R0060:Satb1	UTSW	17	52,047,231 (GRCm39)	missense	probably damaging	1.00
R0067:Satb1	UTSW	17	52,111,364 (GRCm39)	missense	probably damaging	1.00
R0067:Satb1	UTSW	17	52,111,364 (GRCm39)	missense	probably damaging	1.00
R0113:Satb1	UTSW	17	52,089,726 (GRCm39)	nonsense	probably null
R0347:Satb1	UTSW	17	52,046,934 (GRCm39)	nonsense	probably null
R0667:Satb1	UTSW	17	52,089,889 (GRCm39)	missense	probably damaging	1.00
R1436:Satb1	UTSW	17	52,111,391 (GRCm39)	splice site	probably null
R1595:Satb1	UTSW	17	52,089,729 (GRCm39)	missense	possibly damaging	0.82
R1686:Satb1	UTSW	17	52,047,027 (GRCm39)	missense	probably benign	0.08
R1921:Satb1	UTSW	17	52,049,143 (GRCm39)	nonsense	probably null
R1952:Satb1	UTSW	17	52,047,173 (GRCm39)	missense	probably damaging	1.00
R2012:Satb1	UTSW	17	52,089,816 (GRCm39)	nonsense	probably null
R2156:Satb1	UTSW	17	52,047,438 (GRCm39)	missense	probably benign	0.02
R2180:Satb1	UTSW	17	52,110,524 (GRCm39)	missense	probably damaging	0.96
R2959:Satb1	UTSW	17	52,082,331 (GRCm39)	missense	possibly damaging	0.91
R3107:Satb1	UTSW	17	52,089,810 (GRCm39)	missense	possibly damaging	0.95
R3108:Satb1	UTSW	17	52,089,810 (GRCm39)	missense	possibly damaging	0.95
R3814:Satb1	UTSW	17	52,089,935 (GRCm39)	missense	probably damaging	0.98
R4109:Satb1	UTSW	17	52,111,378 (GRCm39)	missense	probably damaging	0.99
R4727:Satb1	UTSW	17	52,111,375 (GRCm39)	missense	probably damaging	1.00
R5209:Satb1	UTSW	17	52,116,235 (GRCm39)	missense	probably benign	0.26
R5815:Satb1	UTSW	17	52,089,981 (GRCm39)	missense	possibly damaging	0.92
R6141:Satb1	UTSW	17	52,082,404 (GRCm39)	missense	possibly damaging	0.93
R6370:Satb1	UTSW	17	52,089,825 (GRCm39)	missense	possibly damaging	0.94
R7371:Satb1	UTSW	17	52,090,008 (GRCm39)	nonsense	probably null
R7409:Satb1	UTSW	17	52,116,217 (GRCm39)	missense	possibly damaging	0.90
R7471:Satb1	UTSW	17	52,090,029 (GRCm39)	missense	probably damaging	0.96
R7568:Satb1	UTSW	17	52,089,752 (GRCm39)	missense	possibly damaging	0.88
R7626:Satb1	UTSW	17	52,074,995 (GRCm39)	missense	probably benign	0.25
R7749:Satb1	UTSW	17	52,074,961 (GRCm39)	missense	possibly damaging	0.70
R7863:Satb1	UTSW	17	52,112,350 (GRCm39)	missense	possibly damaging	0.91
R8339:Satb1	UTSW	17	52,089,977 (GRCm39)	missense	probably damaging	0.97
R8429:Satb1	UTSW	17	52,074,978 (GRCm39)	missense	probably damaging	1.00
R8987:Satb1	UTSW	17	52,112,381 (GRCm39)	missense	probably damaging	1.00
R9160:Satb1	UTSW	17	52,047,053 (GRCm39)	missense	probably benign
R9251:Satb1	UTSW	17	52,112,293 (GRCm39)	missense	probably damaging	1.00
R9656:Satb1	UTSW	17	52,112,264 (GRCm39)	missense	possibly damaging	0.95
Z1088:Satb1	UTSW	17	52,089,980 (GRCm39)	missense	probably damaging	0.98
Z1088:Satb1	UTSW	17	52,089,967 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- AGGAGAACCACTAATTTCCTTGC -3'
(R):5'- ACACTCAGGCAGATTGGAGTG -3'

Sequencing Primer
(F):5'- GTGCTACACTGAATTGGCCAAG -3'
(R):5'- TGCGGTGCGTGGATGAAAAC -3'

Posted On

2016-11-08