Mutagenetix > Incidental Mutation

Incidental Mutation 'R2029:Stag1'

221003

Institutional Source

Beutler Lab

Gene Symbol

Stag1

Ensembl Gene

ENSMUSG00000037286

Gene Name

STAG1 cohesin complex component

Synonyms

SA-1, Scc3

MMRRC Submission

040036-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2029 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

100479762-100840597 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 100668740 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 223 (T223S)

Ref Sequence

ENSEMBL: ENSMUSP00000040724 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000041418] [ENSMUST00000123302] [ENSMUST00000129269] [ENSMUST00000138405] [ENSMUST00000146312] [ENSMUST00000155108]

AlphaFold

Q9D3E6

Predicted Effect

probably damaging
Transcript: ENSMUST00000041418
AA Change: T223S

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

SMART Domains

Protein: ENSMUSP00000040724
Gene: ENSMUSG00000037286
AA Change: T223S

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 damaging
Transcript: ENSMUST00000123302
AA Change: T223S

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000117879
Gene: ENSMUSG00000037286
AA Change: T223S

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: T223S

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000116205
Gene: ENSMUSG00000037286
AA Change: T223S

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 damaging
Transcript: ENSMUST00000138405
AA Change: T223S

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000116322
Gene: ENSMUSG00000037286
AA Change: T223S

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: ENSMUST00000146312
AA Change: T165S

SMART Domains

Protein: ENSMUSP00000116597
Gene: ENSMUSG00000037286
AA Change: T165S

Domain	Start	End	E-Value	Type
low complexity region	32	44	N/A	INTRINSIC
low complexity region	59	72	N/A	INTRINSIC
Pfam:STAG	99	196	4.2e-46	PFAM

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

Meta Mutation Damage Score

0.2674

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 93.8%

Validation Efficiency

98% (97/99)

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: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam18	C	G	8: 25,140,893 (GRCm39)	G286A	probably damaging	Het
Adcy1	G	A	11: 7,089,142 (GRCm39)	A519T	probably benign	Het
Anxa2	T	A	9: 69,371,762 (GRCm39)	S2T	possibly damaging	Het
Ap3m1	G	A	14: 21,089,217 (GRCm39)	S261L	possibly damaging	Het
Baz2b	A	T	2: 59,743,067 (GRCm39)		probably benign	Het
Brdt	T	A	5: 107,507,090 (GRCm39)	S497T	probably benign	Het
Cdh11	A	G	8: 103,406,404 (GRCm39)	F23S	probably benign	Het
Cdh16	A	C	8: 105,344,434 (GRCm39)	L540R	probably damaging	Het
Ces5a	A	T	8: 94,261,205 (GRCm39)	L74Q	probably damaging	Het
Cfap69	A	G	5: 5,654,306 (GRCm39)	S543P	probably damaging	Het
Cfap74	T	C	4: 155,526,538 (GRCm39)	I763T	possibly damaging	Het
Cma1	T	A	14: 56,181,191 (GRCm39)	R58S	possibly damaging	Het
Csmd3	C	T	15: 47,701,975 (GRCm39)	D1599N	probably damaging	Het
Cyld	A	G	8: 89,471,940 (GRCm39)	K857R	probably benign	Het
Cyp3a16	T	C	5: 145,388,667 (GRCm39)	D270G	probably damaging	Het
D1Pas1	T	C	1: 186,700,286 (GRCm39)	S72P	possibly damaging	Het
Ddx3y	T	C	Y: 1,266,389 (GRCm39)	E331G	probably benign	Het
Degs1l	T	A	1: 180,882,496 (GRCm39)	I86K	probably benign	Het
Dis3l2	T	C	1: 86,782,189 (GRCm39)		probably benign	Het
Dop1a	G	T	9: 86,403,418 (GRCm39)	W1539C	probably damaging	Het
Dop1b	A	G	16: 93,566,323 (GRCm39)	K917E	probably benign	Het
Ecpas	G	A	4: 58,844,165 (GRCm39)	R534*	probably null	Het
Efcab3	T	C	11: 104,990,851 (GRCm39)	I5462T	probably damaging	Het
Eif1ad15	A	T	12: 88,288,191 (GRCm39)	S21T	unknown	Het
Epo	A	G	5: 137,483,447 (GRCm39)		probably benign	Het
Figla	T	A	6: 85,997,624 (GRCm39)		probably benign	Het
Flvcr1	T	C	1: 190,753,353 (GRCm39)	D273G	probably benign	Het
Fryl	T	A	5: 73,179,465 (GRCm39)	R304*	probably null	Het
Gcm1	T	G	9: 77,972,326 (GRCm39)	D422E	possibly damaging	Het
Get3	A	T	8: 85,746,403 (GRCm39)	Y148*	probably null	Het
Ggt6	A	G	11: 72,328,367 (GRCm39)	D251G	possibly damaging	Het
Git2	A	G	5: 114,904,511 (GRCm39)		probably null	Het
Gm18856	A	T	13: 14,139,376 (GRCm39)		probably benign	Het
Gm20939	T	A	17: 95,183,252 (GRCm39)		probably benign	Het
Gpr176	A	G	2: 118,109,913 (GRCm39)	Y449H	probably benign	Het
H2-Eb1	A	G	17: 34,533,366 (GRCm39)	E196G	probably damaging	Het
H2-M10.6	A	G	17: 37,124,799 (GRCm39)	T239A	possibly damaging	Het
Haus5	T	C	7: 30,358,825 (GRCm39)	N237S	possibly damaging	Het
Hectd3	T	C	4: 116,857,882 (GRCm39)	M605T	probably damaging	Het
Hps3	T	C	3: 20,084,691 (GRCm39)	I166V	probably benign	Het
Ighv5-21	A	T	12: 114,286,434 (GRCm39)		probably benign	Het
Kdm6b	C	T	11: 69,294,418 (GRCm39)	G1218D	unknown	Het
Klhl30	A	G	1: 91,285,636 (GRCm39)		probably null	Het
Kmt2a	A	T	9: 44,729,747 (GRCm39)	S3523R	probably benign	Het
Lnpep	A	T	17: 17,788,661 (GRCm39)	N481K	probably damaging	Het
Lrp1b	T	C	2: 41,231,861 (GRCm39)	H1203R	probably benign	Het
Lrrc8a	C	T	2: 30,146,661 (GRCm39)	R492W	probably damaging	Het
Magel2	T	A	7: 62,030,342 (GRCm39)	V1082D	unknown	Het
Memo1	A	C	17: 74,552,049 (GRCm39)	H82Q	probably null	Het
Myh13	A	T	11: 67,252,115 (GRCm39)	T1408S	probably benign	Het
Myh2	A	T	11: 67,085,451 (GRCm39)	N1792Y	possibly damaging	Het
Myo1e	A	T	9: 70,275,969 (GRCm39)	N728I	possibly damaging	Het
Myo1e	T	C	9: 70,285,997 (GRCm39)		probably benign	Het
Myo5c	T	C	9: 75,196,337 (GRCm39)		probably benign	Het
Or11l3	T	A	11: 58,516,319 (GRCm39)	L184F	probably damaging	Het
Or1e19	A	G	11: 73,316,188 (GRCm39)	V207A	probably benign	Het
Or2d2b	T	C	7: 106,705,643 (GRCm39)	I142V	probably benign	Het
Or4c11c	T	A	2: 88,661,749 (GRCm39)	M96K	possibly damaging	Het
Or51g1	T	A	7: 102,633,478 (GRCm39)	T298S	probably damaging	Het
Or52e3	T	C	7: 102,868,967 (GRCm39)	F14S	probably damaging	Het
Parp2	C	T	14: 51,047,543 (GRCm39)	A18V	probably benign	Het
Peli1	T	A	11: 21,098,110 (GRCm39)	C282S	probably damaging	Het
Phf8-ps	G	T	17: 33,286,598 (GRCm39)	S68*	probably null	Het
Piezo2	T	C	18: 63,252,006 (GRCm39)	M404V	possibly damaging	Het
Pkn1	T	A	8: 84,404,592 (GRCm39)	Q496L	possibly damaging	Het
Pla2r1	A	T	2: 60,262,317 (GRCm39)	F1093L	probably damaging	Het
Ppp2r3d	A	G	9: 101,022,680 (GRCm39)	V323A	probably damaging	Het
Pramel16	T	A	4: 143,676,453 (GRCm39)	Y217F	probably benign	Het
Prg2	C	T	2: 84,812,342 (GRCm39)		probably benign	Het
Ptprb	G	A	10: 116,182,958 (GRCm39)	G1545S	probably benign	Het
Rbm19	A	G	5: 120,258,307 (GRCm39)	D174G	possibly damaging	Het
Rhbdf2	T	A	11: 116,491,974 (GRCm39)	T526S	probably damaging	Het
Rpusd4	A	G	9: 35,179,310 (GRCm39)	N42S	probably benign	Het
Ryr3	T	A	2: 112,477,361 (GRCm39)	Q4455L	possibly damaging	Het
Sema4a	G	T	3: 88,358,668 (GRCm39)	H30Q	probably damaging	Het
Skint1	G	A	4: 111,878,653 (GRCm39)		probably null	Het
Slc1a3	A	G	15: 8,675,153 (GRCm39)	V284A	probably benign	Het
Slc30a9	A	T	5: 67,497,318 (GRCm39)	K288*	probably null	Het
Slc36a1	G	T	11: 55,119,164 (GRCm39)	A380S	probably benign	Het
Slc47a1	G	A	11: 61,268,833 (GRCm39)		probably benign	Het
Snx19	A	T	9: 30,340,296 (GRCm39)	E478V	probably benign	Het
Spag6	T	C	2: 18,738,916 (GRCm39)		probably benign	Het
Terb1	A	T	8: 105,224,732 (GRCm39)		probably benign	Het
Terf1	A	G	1: 15,876,170 (GRCm39)	D90G	possibly damaging	Het
Tex15	A	G	8: 34,061,302 (GRCm39)	D518G	probably damaging	Het
Tmem174	T	A	13: 98,773,546 (GRCm39)	M95L	possibly damaging	Het
Tnnt3	GTCCAGGCATCTC	GTC	7: 142,066,364 (GRCm39)		probably benign	Het
Usp28	A	G	9: 48,896,803 (GRCm39)	D8G	probably benign	Het
Vmn2r105	T	C	17: 20,444,840 (GRCm39)	T551A	probably damaging	Het
Vmn2r107	A	G	17: 20,595,549 (GRCm39)	I701V	probably benign	Het
Vmn2r13	A	C	5: 109,339,943 (GRCm39)	F11V	probably benign	Het
Vmn2r85	G	C	10: 130,261,443 (GRCm39)	S298*	probably null	Het
Wdr6	C	G	9: 108,452,554 (GRCm39)	W443S	probably damaging	Het
Wipi1	A	G	11: 109,474,016 (GRCm39)	V210A	probably damaging	Het
Zfp317	A	G	9: 19,556,532 (GRCm39)	T47A	probably benign	Het
Zfp61	T	C	7: 23,991,714 (GRCm39)	T146A	probably benign	Het
Zfp964	A	G	8: 70,116,567 (GRCm39)	E389G	unknown	Het
Zfyve16	T	C	13: 92,640,985 (GRCm39)	D1253G	probably damaging	Het
Zpld2	T	C	4: 133,929,669 (GRCm39)	K212R	possibly damaging	Het
Zswim7	G	A	11: 62,158,299 (GRCm39)		probably benign	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
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
R2504:Stag1	UTSW	9	100,748,263 (GRCm39)	missense	probably damaging	0.99
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'- TAGGACAGTGGTGACTACCC -3'
(R):5'- AGGCTGTCAAATAGCAAGTAGC -3'

Sequencing Primer
(F):5'- AGTGGTGACTACCCCCTTACAATG -3'
(R):5'- GCACTAACTAAATTAACCTTA -3'

Posted On

2014-08-25