Mutagenetix > Incidental Mutation

Incidental Mutation 'R2504:Stag1'

252179

Institutional Source

Beutler Lab

Gene Symbol

Stag1

Ensembl Gene

ENSMUSG00000037286

Gene Name

STAG1 cohesin complex component

Synonyms

SA-1, Scc3

MMRRC Submission

040412-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2504 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

100479762-100840597 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 100748263 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Isoleucine at position 475 (S475I)

Ref Sequence

ENSEMBL: ENSMUSP00000040724 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000041418] [ENSMUST00000123302] [ENSMUST00000129269] [ENSMUST00000138405] [ENSMUST00000155108]

AlphaFold

Q9D3E6

Predicted Effect

probably damaging
Transcript: ENSMUST00000041418
AA Change: S475I

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000040724
Gene: ENSMUSG00000037286
AA Change: S475I

Domain	Start	End	E-Value	Type
low complexity region	32	44	N/A	INTRINSIC
low complexity region	59	72	N/A	INTRINSIC
Pfam:STAG	157	276	1.5e-50	PFAM
SCOP:d1qbkb_	279	850	4e-5	SMART
low complexity region	1062	1081	N/A	INTRINSIC
low complexity region	1107	1120	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000123302

SMART Domains

Protein: ENSMUSP00000117879
Gene: ENSMUSG00000037286

Domain	Start	End	E-Value	Type
low complexity region	32	44	N/A	INTRINSIC
low complexity region	59	72	N/A	INTRINSIC
Pfam:STAG	157	276	2.9e-51	PFAM
low complexity region	303	315	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000129269
AA Change: S475I

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000116205
Gene: ENSMUSG00000037286
AA Change: S475I

Domain	Start	End	E-Value	Type
low complexity region	32	44	N/A	INTRINSIC
low complexity region	59	72	N/A	INTRINSIC
Pfam:STAG	160	274	3.8e-41	PFAM
SCOP:d1qbkb_	279	850	3e-5	SMART
low complexity region	1062	1081	N/A	INTRINSIC
low complexity region	1107	1120	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000138405

SMART Domains

Protein: ENSMUSP00000116322
Gene: ENSMUSG00000037286

Domain	Start	End	E-Value	Type
low complexity region	32	44	N/A	INTRINSIC
low complexity region	59	72	N/A	INTRINSIC
Pfam:STAG	157	276	1.5e-51	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000146934
AA Change: S85I

SMART Domains

Protein: ENSMUSP00000120974
Gene: ENSMUSG00000037286
AA Change: S85I

Domain	Start	End	E-Value	Type
low complexity region	673	692	N/A	INTRINSIC
low complexity region	718	731	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149771

Predicted Effect

probably benign
Transcript: ENSMUST00000155108

SMART Domains

Protein: ENSMUSP00000118952
Gene: ENSMUSG00000037286

Domain	Start	End	E-Value	Type
low complexity region	32	44	N/A	INTRINSIC
low complexity region	59	72	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.4%
20x: 95.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the SCC3 family and is expressed in the nucleus. It encodes a component of cohesin, a multisubunit protein complex that provides sister chromatid cohesion along the length of a chromosome from DNA replication through prophase and prometaphase, after which it is dissociated in preparation for segregation during anaphase. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mouse embryos homozygous for a null mutation show developmental delay and die before birth. Heterozygous animals have shorter lifespan and earlier onset of tumourigenesis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aatk	T	C	11: 119,909,681 (GRCm39)	D28G	probably benign	Het
Abcg1	T	A	17: 31,311,369 (GRCm39)	S125T	probably damaging	Het
Actbl2	T	C	13: 111,392,717 (GRCm39)	S351P	possibly damaging	Het
Ankrd34b	A	G	13: 92,575,569 (GRCm39)		probably null	Het
BC051665	C	T	13: 60,930,468 (GRCm39)	V295I	probably benign	Het
C1qtnf2	A	G	11: 43,381,983 (GRCm39)	N265S	probably damaging	Het
Ccdc14	C	T	16: 34,542,220 (GRCm39)	R573*	probably null	Het
Cd55b	A	T	1: 130,337,612 (GRCm39)	Y247N	probably damaging	Het
Celsr2	A	T	3: 108,320,907 (GRCm39)	V635E	probably benign	Het
Clec16a	T	C	16: 10,377,551 (GRCm39)		probably benign	Het
Clec4b1	A	G	6: 123,042,904 (GRCm39)	Y41C	probably damaging	Het
Cntn5	A	T	9: 10,172,126 (GRCm39)	D19E	probably benign	Het
Cop1	A	G	1: 159,060,375 (GRCm39)	N53S	probably damaging	Het
Cplane1	G	A	15: 8,248,700 (GRCm39)	E1750K	probably damaging	Het
Csad	A	T	15: 102,097,102 (GRCm39)	M1K	probably null	Het
Cyb5rl	A	G	4: 106,938,142 (GRCm39)	I200V	probably benign	Het
Cyp26a1	A	G	19: 37,686,790 (GRCm39)	T81A	probably damaging	Het
Cyp2d12	A	T	15: 82,443,237 (GRCm39)	H433L	probably benign	Het
D7Ertd443e	T	A	7: 133,951,208 (GRCm39)		probably null	Het
Dennd1b	A	G	1: 139,097,908 (GRCm39)		probably benign	Het
Dmap1	G	T	4: 117,532,495 (GRCm39)	T357K	probably damaging	Het
Dzip1	G	T	14: 119,118,456 (GRCm39)	T759K	probably benign	Het
Elmo2	A	G	2: 165,140,607 (GRCm39)	V300A	probably damaging	Het
Eml5	T	C	12: 98,810,364 (GRCm39)	D864G	possibly damaging	Het
Ep400	A	G	5: 110,816,511 (GRCm39)	V2670A	probably damaging	Het
Epha3	T	A	16: 63,423,988 (GRCm39)	I534F	probably damaging	Het
Epha4	A	C	1: 77,359,628 (GRCm39)	Y742D	probably damaging	Het
Ergic2	A	G	6: 148,106,272 (GRCm39)		probably null	Het
Ero1a	A	T	14: 45,536,545 (GRCm39)		probably null	Het
Fam229a	A	G	4: 129,385,279 (GRCm39)	D70G	probably damaging	Het
Fbn2	C	T	18: 58,226,431 (GRCm39)	R781Q	probably damaging	Het
Fbxo16	A	T	14: 65,508,163 (GRCm39)		probably benign	Het
Fbxo39	T	A	11: 72,208,111 (GRCm39)	S154R	probably benign	Het
Fer	T	A	17: 64,298,575 (GRCm39)		probably null	Het
Filip1l	A	T	16: 57,391,410 (GRCm39)	D428V	probably damaging	Het
Filip1l	A	G	16: 57,391,025 (GRCm39)	I538V	possibly damaging	Het
Fsip2	T	C	2: 82,809,954 (GRCm39)	I2091T	possibly damaging	Het
Glyat	A	C	19: 12,628,762 (GRCm39)	T186P	possibly damaging	Het
Gm10604	A	G	4: 11,980,083 (GRCm39)	S74P	unknown	Het
Gm4787	T	G	12: 81,425,911 (GRCm39)	K82N	possibly damaging	Het
Hectd4	T	C	5: 121,358,683 (GRCm39)	I50T	unknown	Het
Hectd4	T	C	5: 121,402,030 (GRCm39)	S373P	possibly damaging	Het
Hmcn1	A	T	1: 150,562,618 (GRCm39)	C2313*	probably null	Het
Hrob	T	C	11: 102,146,122 (GRCm39)	Y133H	possibly damaging	Het
Igfn1	A	T	1: 135,897,054 (GRCm39)	S1171T	probably benign	Het
Ints8	T	C	4: 11,241,642 (GRCm39)	D267G	probably benign	Het
Itln1	A	G	1: 171,356,727 (GRCm39)	C251R	probably damaging	Het
Jcad	C	T	18: 4,674,026 (GRCm39)	T596M	probably damaging	Het
Kcnj16	C	T	11: 110,916,409 (GRCm39)	T357M	probably benign	Het
Kif13a	G	A	13: 46,967,676 (GRCm39)	T346M	probably damaging	Het
Klhl24	G	A	16: 19,938,917 (GRCm39)	A491T	probably benign	Het
Kntc1	C	T	5: 123,916,410 (GRCm39)	Q748*	probably null	Het
Krt25	T	A	11: 99,208,122 (GRCm39)	K369*	probably null	Het
Krt75	C	T	15: 101,476,466 (GRCm39)	R433Q	probably benign	Het
Krt76	A	G	15: 101,793,293 (GRCm39)	F582L	unknown	Het
Lysmd1	G	A	3: 95,045,708 (GRCm39)	V182I	probably benign	Het
Mab21l2	T	A	3: 86,454,862 (GRCm39)	E46V	probably damaging	Het
Magi2	A	T	5: 20,563,934 (GRCm39)	K355N	probably damaging	Het
Marchf10	T	C	11: 105,276,398 (GRCm39)	D630G	probably damaging	Het
Mast4	A	T	13: 102,875,147 (GRCm39)	I1215N	probably damaging	Het
Nckap1	G	A	2: 80,360,562 (GRCm39)	T523I	probably benign	Het
Nexmif	T	A	X: 103,127,999 (GRCm39)	D1306V	probably damaging	Het
Nfkb1	A	C	3: 135,295,090 (GRCm39)	I918R	possibly damaging	Het
Nt5el	A	G	13: 105,246,250 (GRCm39)	I270M	probably benign	Het
Nup50	A	T	15: 84,817,859 (GRCm39)	T93S	probably benign	Het
Nwd2	T	C	5: 63,961,717 (GRCm39)	Y434H	probably benign	Het
Or13a28	T	C	7: 140,218,397 (GRCm39)	V261A	probably benign	Het
Osbpl1a	C	A	18: 13,038,088 (GRCm39)	V288L	probably benign	Het
Pan3	A	G	5: 147,463,846 (GRCm39)	E562G	possibly damaging	Het
Pappa	T	A	4: 65,099,126 (GRCm39)	Y548*	probably null	Het
Phf3	A	T	1: 30,849,870 (GRCm39)	L1181Q	probably damaging	Het
Phip	T	C	9: 82,797,392 (GRCm39)	H537R	possibly damaging	Het
Pkhd1l1	T	C	15: 44,348,824 (GRCm39)	I240T	probably damaging	Het
Pole	G	A	5: 110,438,368 (GRCm39)		probably null	Het
Polq	T	A	16: 36,832,304 (GRCm39)	S15T	unknown	Het
Prrt2	T	C	7: 126,619,396 (GRCm39)	E23G	possibly damaging	Het
Prss37	A	T	6: 40,494,760 (GRCm39)		probably null	Het
Prune2	T	C	19: 16,977,400 (GRCm39)	L45P	probably damaging	Het
Psd	A	T	19: 46,313,352 (GRCm39)	M6K	possibly damaging	Het
Psmd1	A	G	1: 86,017,719 (GRCm39)	E510G	possibly damaging	Het
Ptch1	T	G	13: 63,672,773 (GRCm39)	E944A	probably benign	Het
Pxdn	T	A	12: 30,053,405 (GRCm39)	I1194N	probably damaging	Het
Rbp3	C	T	14: 33,677,975 (GRCm39)	T641M	probably damaging	Het
Rgmb	C	A	17: 16,027,909 (GRCm39)	R270L	probably benign	Het
Rpgrip1l	A	G	8: 92,007,344 (GRCm39)		probably null	Het
Rps2	G	A	17: 24,939,353 (GRCm39)		probably benign	Het
Rsbn1l	G	T	5: 21,107,364 (GRCm39)	A550E	probably damaging	Het
S1pr4	C	T	10: 81,335,138 (GRCm39)	R112H	probably benign	Het
Scfd2	T	C	5: 74,691,838 (GRCm39)	N148S	probably damaging	Het
Scin	C	T	12: 40,131,705 (GRCm39)	M276I	probably benign	Het
Sec24d	T	C	3: 123,147,255 (GRCm39)	I708T	possibly damaging	Het
Skint11	T	A	4: 114,086,009 (GRCm39)	F41I	possibly damaging	Het
Slc15a4	A	T	5: 127,694,303 (GRCm39)	F44Y	possibly damaging	Het
Slc6a18	A	G	13: 73,823,925 (GRCm39)	Y72H	probably benign	Het
Slc7a11	A	T	3: 50,332,195 (GRCm39)		probably null	Het
Slc7a14	G	T	3: 31,291,650 (GRCm39)	N209K	possibly damaging	Het
Sstr2	T	C	11: 113,515,257 (GRCm39)	C59R	probably damaging	Het
Stab1	A	G	14: 30,884,997 (GRCm39)		probably null	Het
Stxbp5l	A	G	16: 36,936,029 (GRCm39)	Y1183H	probably damaging	Het
Svep1	A	T	4: 58,135,628 (GRCm39)		probably null	Het
Tm9sf2	A	G	14: 122,396,096 (GRCm39)	T653A	probably benign	Het
Tmeff1	T	C	4: 48,662,059 (GRCm39)	S366P	possibly damaging	Het
Tnnt2	G	T	1: 135,779,803 (GRCm39)	W300L	probably damaging	Het
Traj32	A	G	14: 54,423,560 (GRCm39)		probably benign	Het
Trp53bp2	A	T	1: 182,269,204 (GRCm39)	M223L	probably benign	Het
Tsga10	G	A	1: 37,854,758 (GRCm39)	T246M	probably damaging	Het
Txn2	A	T	15: 77,810,870 (GRCm39)		probably benign	Het
Ubr3	T	A	2: 69,768,542 (GRCm39)	F450I	probably damaging	Het
Usp47	T	C	7: 111,703,677 (GRCm39)		probably null	Het
Vars2	C	T	17: 35,975,685 (GRCm39)	R244Q	probably damaging	Het
Xrra1	T	A	7: 99,546,803 (GRCm39)	F251L	probably damaging	Het
Zfp804a	G	A	2: 82,087,863 (GRCm39)	R564Q	probably benign	Het
Zfp983	T	C	17: 21,877,883 (GRCm39)	C29R	probably damaging	Het

Other mutations in Stag1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00649:Stag1	APN	9	100,658,861 (GRCm39)	missense	probably damaging	1.00
IGL01010:Stag1	APN	9	100,827,986 (GRCm39)	missense	probably benign	0.06
IGL01012:Stag1	APN	9	100,737,912 (GRCm39)	missense	possibly damaging	0.47
IGL01025:Stag1	APN	9	100,833,710 (GRCm39)	missense	possibly damaging	0.95
IGL01307:Stag1	APN	9	100,833,841 (GRCm39)	intron	probably benign
IGL02149:Stag1	APN	9	100,769,442 (GRCm39)	missense	probably benign	0.09
IGL02608:Stag1	APN	9	100,639,822 (GRCm39)	missense	probably null	0.99
IGL03008:Stag1	APN	9	100,658,844 (GRCm39)	missense	probably damaging	1.00
IGL03210:Stag1	APN	9	100,727,129 (GRCm39)	missense	possibly damaging	0.63
eto_o	UTSW	9	100,678,769 (GRCm39)	missense	probably damaging	1.00
PIT4280001:Stag1	UTSW	9	100,824,769 (GRCm39)	missense	possibly damaging	0.95
R0070:Stag1	UTSW	9	100,838,461 (GRCm39)	missense	probably null	1.00
R0070:Stag1	UTSW	9	100,838,461 (GRCm39)	missense	probably null	1.00
R0349:Stag1	UTSW	9	100,658,837 (GRCm39)	missense	probably damaging	0.98
R0479:Stag1	UTSW	9	100,810,144 (GRCm39)	missense	probably benign	0.00
R0531:Stag1	UTSW	9	100,836,300 (GRCm39)	makesense	probably null
R0962:Stag1	UTSW	9	100,678,880 (GRCm39)	missense	probably damaging	1.00
R0976:Stag1	UTSW	9	100,812,069 (GRCm39)	critical splice donor site	probably null
R0976:Stag1	UTSW	9	100,658,877 (GRCm39)	missense	probably damaging	0.98
R1170:Stag1	UTSW	9	100,770,506 (GRCm39)	intron	probably benign
R1499:Stag1	UTSW	9	100,769,426 (GRCm39)	intron	probably benign
R1499:Stag1	UTSW	9	100,737,885 (GRCm39)	missense	possibly damaging	0.77
R1644:Stag1	UTSW	9	100,762,953 (GRCm39)	intron	probably benign
R1747:Stag1	UTSW	9	100,770,353 (GRCm39)	missense	probably benign
R1799:Stag1	UTSW	9	100,835,515 (GRCm39)	splice site	probably null
R1807:Stag1	UTSW	9	100,790,719 (GRCm39)	missense	probably benign	0.34
R1978:Stag1	UTSW	9	100,770,139 (GRCm39)	missense	probably benign	0.03
R2029:Stag1	UTSW	9	100,668,740 (GRCm39)	missense	probably damaging	1.00
R2161:Stag1	UTSW	9	100,771,648 (GRCm39)	missense	probably damaging	1.00
R2300:Stag1	UTSW	9	100,594,553 (GRCm39)	missense	possibly damaging	0.92
R2327:Stag1	UTSW	9	100,668,666 (GRCm39)	missense	possibly damaging	0.81
R2426:Stag1	UTSW	9	100,727,169 (GRCm39)	critical splice donor site	probably null
R2448:Stag1	UTSW	9	100,770,462 (GRCm39)	missense	probably benign	0.42
R3713:Stag1	UTSW	9	100,771,671 (GRCm39)	missense	probably benign	0.01
R3835:Stag1	UTSW	9	100,620,035 (GRCm39)	missense	probably damaging	0.97
R3862:Stag1	UTSW	9	100,826,838 (GRCm39)	missense	probably benign	0.02
R4398:Stag1	UTSW	9	100,838,659 (GRCm39)	utr 3 prime	probably benign
R4568:Stag1	UTSW	9	100,730,722 (GRCm39)	missense	probably damaging	1.00
R4651:Stag1	UTSW	9	100,678,769 (GRCm39)	missense	probably damaging	1.00
R4652:Stag1	UTSW	9	100,678,769 (GRCm39)	missense	probably damaging	1.00
R4653:Stag1	UTSW	9	100,678,769 (GRCm39)	missense	probably damaging	1.00
R4675:Stag1	UTSW	9	100,730,758 (GRCm39)	missense	probably damaging	1.00
R4709:Stag1	UTSW	9	100,620,092 (GRCm39)	missense	probably damaging	0.99
R4924:Stag1	UTSW	9	100,678,808 (GRCm39)	missense	possibly damaging	0.67
R5018:Stag1	UTSW	9	100,833,672 (GRCm39)	missense	probably benign	0.00
R5435:Stag1	UTSW	9	100,835,603 (GRCm39)	missense	probably benign	0.03
R5460:Stag1	UTSW	9	100,838,506 (GRCm39)	splice site	probably null
R5805:Stag1	UTSW	9	100,678,831 (GRCm39)	missense	probably damaging	1.00
R6127:Stag1	UTSW	9	100,833,750 (GRCm39)	missense	probably benign	0.05
R6313:Stag1	UTSW	9	100,639,786 (GRCm39)	missense	probably damaging	1.00
R6597:Stag1	UTSW	9	100,769,473 (GRCm39)	missense	probably benign	0.01
R6807:Stag1	UTSW	9	100,826,903 (GRCm39)	missense	probably damaging	1.00
R7099:Stag1	UTSW	9	100,826,879 (GRCm39)	missense	probably benign	0.02
R7167:Stag1	UTSW	9	100,827,942 (GRCm39)	missense	probably benign	0.05
R7395:Stag1	UTSW	9	100,678,781 (GRCm39)	missense	probably damaging	0.99
R7504:Stag1	UTSW	9	100,770,381 (GRCm39)	missense	probably benign	0.09
R7663:Stag1	UTSW	9	100,620,191 (GRCm39)	missense	probably damaging	0.98
R7769:Stag1	UTSW	9	100,826,880 (GRCm39)	missense	possibly damaging	0.86
R8245:Stag1	UTSW	9	100,811,946 (GRCm39)	missense	probably benign	0.01
R8343:Stag1	UTSW	9	100,639,819 (GRCm39)	missense	possibly damaging	0.95
R8473:Stag1	UTSW	9	100,762,840 (GRCm39)	missense	probably damaging	1.00
R8709:Stag1	UTSW	9	100,772,975 (GRCm39)	intron	probably benign
R8925:Stag1	UTSW	9	100,587,298 (GRCm39)	missense	possibly damaging	0.46
R8927:Stag1	UTSW	9	100,587,298 (GRCm39)	missense	possibly damaging	0.46
R8951:Stag1	UTSW	9	100,762,854 (GRCm39)	missense	probably damaging	1.00
R9138:Stag1	UTSW	9	100,829,335 (GRCm39)	missense	probably benign	0.01
R9233:Stag1	UTSW	9	100,812,024 (GRCm39)	missense	probably benign	0.00
R9246:Stag1	UTSW	9	100,770,329 (GRCm39)	missense	probably benign	0.00
R9419:Stag1	UTSW	9	100,811,967 (GRCm39)	missense	probably benign
R9442:Stag1	UTSW	9	100,836,306 (GRCm39)	missense	probably damaging	1.00
R9694:Stag1	UTSW	9	100,810,151 (GRCm39)	missense	probably benign	0.05
R9740:Stag1	UTSW	9	100,587,288 (GRCm39)	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- TTCCTCATGTTGAACTGTGTAAGA -3'
(R):5'- GCATGTAAAACTGGCATTCTATAAACA -3'

Sequencing Primer
(F):5'- TAGCATGTGACTGAAAGCTCAAC -3'
(R):5'- GGAAAAGGCTTGTTTTCCTAT -3'

Posted On

2014-12-04