Mutagenetix > Incidental Mutation

Incidental Mutation 'R1509:Smc6'

168163

Institutional Source

Beutler Lab

Gene Symbol

Smc6

Ensembl Gene

ENSMUSG00000020608

Gene Name

structural maintenance of chromosomes 6

Synonyms

3830418C19Rik, Smc6l1, 2810489L22Rik

MMRRC Submission

039556-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1509 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

11315887-11369786 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 11329734 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Asparagine at position 164 (S164N)

Ref Sequence

ENSEMBL: ENSMUSP00000151976 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020931] [ENSMUST00000217906] [ENSMUST00000218022] [ENSMUST00000218866] [ENSMUST00000219776]

AlphaFold

Q924W5

Predicted Effect

possibly damaging
Transcript: ENSMUST00000020931
AA Change: S164N

PolyPhen 2 Score 0.546 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000020931
Gene: ENSMUSG00000020608
AA Change: S164N

Domain	Start	End	E-Value	Type
Pfam:SMC_N	53	1077	4.7e-17	PFAM
Pfam:AAA_15	54	438	3.1e-9	PFAM
Pfam:AAA_23	56	398	5e-12	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000217906

Predicted Effect

probably benign
Transcript: ENSMUST00000218022

Predicted Effect

possibly damaging
Transcript: ENSMUST00000218866
AA Change: S164N

PolyPhen 2 Score 0.546 (Sensitivity: 0.88; Specificity: 0.91)

Predicted Effect

probably benign
Transcript: ENSMUST00000219776

Meta Mutation Damage Score

0.1642

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.4%
20x: 93.1%

Validation Efficiency

99% (89/90)

MGI Phenotype

PHENOTYPE: Mice homozygous for a gene trap allele exhibit poor embryonic development and embryonic lethality by E105. Mice homozygous for a hypomorphic allele exhibit decreased body weight and weight, decreased litter size and partial lethality. Mice homozygous for a point mutation exhibit a milder phenotype. [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
2210408I21Rik	T	C	13: 77,340,766 (GRCm39)	S132P	probably benign	Het
AC153895.1	T	C	6: 50,020,451 (GRCm39)	R54G	unknown	Het
Acot12	G	A	13: 91,919,994 (GRCm39)		probably null	Het
Adhfe1	T	A	1: 9,623,671 (GRCm39)	D98E	probably benign	Het
Ago2	A	G	15: 72,988,213 (GRCm39)	F594S	probably damaging	Het
Aldh18a1	A	G	19: 40,545,927 (GRCm39)	I620T	probably damaging	Het
Aspscr1	C	A	11: 120,592,342 (GRCm39)	A294D	probably damaging	Het
Bod1l	C	G	5: 41,976,883 (GRCm39)	R1477T	probably damaging	Het
Ccdc18	C	A	5: 108,336,844 (GRCm39)	A741D	possibly damaging	Het
Ces4a	G	A	8: 105,864,729 (GRCm39)	G69S	probably damaging	Het
Cfap52	C	T	11: 67,829,819 (GRCm39)	V317I	probably benign	Het
Cgn	A	T	3: 94,681,568 (GRCm39)	L509Q	probably benign	Het
Crb2	A	G	2: 37,676,631 (GRCm39)	H204R	probably benign	Het
Cspg4b	A	G	13: 113,504,790 (GRCm39)	N431S	probably damaging	Het
Ddx39a	G	A	8: 84,446,527 (GRCm39)	V99M	probably damaging	Het
Dis3l2	T	A	1: 86,948,808 (GRCm39)	C582S	possibly damaging	Het
Dmbt1	G	A	7: 130,676,061 (GRCm39)		probably benign	Het
Dnah6	T	C	6: 73,004,425 (GRCm39)	E3846G	probably damaging	Het
Dstyk	A	G	1: 132,384,084 (GRCm39)	E655G	probably damaging	Het
Epha4	T	C	1: 77,357,523 (GRCm39)	Y825C	probably damaging	Het
Esp36	T	A	17: 38,728,173 (GRCm39)	N36I	probably damaging	Het
Fabp3	C	T	4: 130,206,180 (GRCm39)	T57I	probably benign	Het
Fem1c	A	G	18: 46,657,280 (GRCm39)	S145P	probably benign	Het
Galnt13	T	C	2: 54,623,094 (GRCm39)	I80T	probably damaging	Het
Gm5698	T	C	1: 31,016,728 (GRCm39)	T108A	probably benign	Het
Hipk3	A	G	2: 104,271,607 (GRCm39)	S442P	probably benign	Het
Hmcn2	T	A	2: 31,204,491 (GRCm39)	V22D	possibly damaging	Het
Hspg2	C	T	4: 137,238,552 (GRCm39)		probably benign	Het
Ide	A	G	19: 37,262,603 (GRCm39)		probably null	Het
Ifnar1	C	A	16: 91,300,384 (GRCm39)	P462Q	probably damaging	Het
Itgb2l	T	A	16: 96,228,049 (GRCm39)	I485F	probably benign	Het
Jakmip3	C	T	7: 138,629,505 (GRCm39)	R549W	possibly damaging	Het
Lrrc36	A	G	8: 106,187,761 (GRCm39)	Q680R	probably damaging	Het
Lysmd3	T	G	13: 81,817,390 (GRCm39)	H122Q	probably benign	Het
Macf1	C	A	4: 123,577,802 (GRCm39)	V61L	possibly damaging	Het
Map1b	T	C	13: 99,568,036 (GRCm39)	T1562A	unknown	Het
Map3k20	A	T	2: 72,194,968 (GRCm39)		probably benign	Het
Mroh8	A	G	2: 157,075,125 (GRCm39)	V457A	probably benign	Het
Mrpl40	T	A	16: 18,694,159 (GRCm39)		probably null	Het
Ms4a10	C	T	19: 10,941,472 (GRCm39)	V166I	probably benign	Het
Mycl	A	G	4: 122,894,100 (GRCm39)	D300G	probably damaging	Het
Naca	T	A	10: 127,879,266 (GRCm39)		probably benign	Het
Ncoa4	T	C	14: 31,895,391 (GRCm39)	S172P	probably damaging	Het
Nfatc3	T	C	8: 106,810,486 (GRCm39)	F421L	possibly damaging	Het
Nucb1	C	A	7: 45,144,649 (GRCm39)	K301N	probably benign	Het
Or1af1	A	G	2: 37,109,966 (GRCm39)	H155R	probably damaging	Het
Or52ae9	A	T	7: 103,390,243 (GRCm39)	M68K	probably benign	Het
Or5b99	T	A	19: 12,976,815 (GRCm39)	I155N	possibly damaging	Het
Panx1	A	T	9: 14,921,341 (GRCm39)	V178E	possibly damaging	Het
Pkd1l3	G	A	8: 110,367,402 (GRCm39)	V1210I	probably damaging	Het
Polr2a	A	T	11: 69,638,039 (GRCm39)	H143Q	possibly damaging	Het
Potefam1	A	T	2: 111,048,972 (GRCm39)	M269K	probably benign	Het
Prdm12	G	A	2: 31,544,186 (GRCm39)	R263H	probably damaging	Het
Prkdc	A	C	16: 15,549,430 (GRCm39)	K1998T	probably damaging	Het
Rab11fip1	A	T	8: 27,643,051 (GRCm39)	S583T	probably damaging	Het
Rnf157	T	A	11: 116,237,921 (GRCm39)	T567S	probably benign	Het
Rp1	T	C	1: 4,417,917 (GRCm39)	K1065R	probably damaging	Het
Rp1	A	G	1: 4,418,760 (GRCm39)	I784T	probably benign	Het
Rps10	A	C	17: 27,850,182 (GRCm39)	F150V	probably benign	Het
Rrp12	A	T	19: 41,870,639 (GRCm39)	F499I	probably damaging	Het
Sez6l2	G	A	7: 126,562,535 (GRCm39)	R604H	probably damaging	Het
Slc25a21	G	T	12: 56,904,864 (GRCm39)	Q57K	probably benign	Het
Slc27a2	A	G	2: 126,395,234 (GRCm39)	T54A	possibly damaging	Het
Slc9a9	T	A	9: 95,111,011 (GRCm39)	S610T	probably benign	Het
Smc1b	A	T	15: 84,970,335 (GRCm39)	S973T	probably benign	Het
Sp1	A	G	15: 102,316,314 (GRCm39)	T32A	possibly damaging	Het
Spen	T	C	4: 141,202,946 (GRCm39)	I1894V	probably benign	Het
Spen	T	C	4: 141,203,011 (GRCm39)	K1872R	possibly damaging	Het
Stab1	C	A	14: 30,873,541 (GRCm39)		probably benign	Het
Taar7d	T	G	10: 23,904,102 (GRCm39)	F328C	probably damaging	Het
Ticam1	A	T	17: 56,578,113 (GRCm39)	S327R	probably benign	Het
Tmem248	C	T	5: 130,258,295 (GRCm39)		probably benign	Het
Tom1	T	C	8: 75,781,259 (GRCm39)	S83P	probably damaging	Het
Txk	T	A	5: 72,856,453 (GRCm39)	Y446F	probably damaging	Het
Ubap1l	T	A	9: 65,279,237 (GRCm39)	C179S	probably benign	Het
Utrn	T	C	10: 12,331,185 (GRCm39)	E474G	possibly damaging	Het
Vmn2r14	T	C	5: 109,363,862 (GRCm39)	M685V	probably benign	Het
Vmn2r7	A	T	3: 64,623,881 (GRCm39)	Y146*	probably null	Het
Wdr1	G	A	5: 38,697,905 (GRCm39)	T220M	probably damaging	Het
Xpo7	T	C	14: 70,915,582 (GRCm39)	D726G	probably damaging	Het
Zbtb14	C	G	17: 69,694,759 (GRCm39)	I152M	probably benign	Het
Zbtb3	A	G	19: 8,780,771 (GRCm39)	D128G	probably damaging	Het
Zeb1os1	A	G	18: 5,583,794 (GRCm39)		noncoding transcript	Het
Zfp462	T	A	4: 55,007,667 (GRCm39)	D35E	probably damaging	Het
Zfp467	A	G	6: 48,415,621 (GRCm39)	S344P	possibly damaging	Het
Zfpm1	A	T	8: 123,034,285 (GRCm39)	D73V	possibly damaging	Het

Other mutations in Smc6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00433:Smc6	APN	12	11,349,264 (GRCm39)	missense	possibly damaging	0.48
IGL00562:Smc6	APN	12	11,351,532 (GRCm39)	missense	probably benign	0.02
IGL00563:Smc6	APN	12	11,351,532 (GRCm39)	missense	probably benign	0.02
IGL01420:Smc6	APN	12	11,341,659 (GRCm39)	missense	probably benign	0.27
IGL02299:Smc6	APN	12	11,340,752 (GRCm39)	missense	probably benign	0.00
R0207:Smc6	UTSW	12	11,333,179 (GRCm39)	unclassified	probably benign
R0365:Smc6	UTSW	12	11,333,175 (GRCm39)	critical splice donor site	probably null
R0669:Smc6	UTSW	12	11,339,165 (GRCm39)	missense	probably benign	0.41
R0732:Smc6	UTSW	12	11,340,818 (GRCm39)	missense	probably damaging	0.96
R1398:Smc6	UTSW	12	11,321,880 (GRCm39)	splice site	probably benign
R1739:Smc6	UTSW	12	11,367,854 (GRCm39)	missense	probably benign	0.05
R1775:Smc6	UTSW	12	11,359,270 (GRCm39)	missense	probably benign	0.00
R1815:Smc6	UTSW	12	11,344,602 (GRCm39)	critical splice donor site	probably null
R1937:Smc6	UTSW	12	11,349,399 (GRCm39)	missense	probably benign	0.06
R2090:Smc6	UTSW	12	11,339,987 (GRCm39)	missense	probably benign	0.08
R2885:Smc6	UTSW	12	11,326,294 (GRCm39)	missense	probably damaging	0.99
R2886:Smc6	UTSW	12	11,326,294 (GRCm39)	missense	probably damaging	0.99
R2991:Smc6	UTSW	12	11,339,982 (GRCm39)	missense	probably damaging	0.96
R3825:Smc6	UTSW	12	11,351,517 (GRCm39)	splice site	probably benign
R3967:Smc6	UTSW	12	11,348,327 (GRCm39)	missense	probably benign	0.13
R3975:Smc6	UTSW	12	11,324,075 (GRCm39)	missense	probably damaging	0.99
R4660:Smc6	UTSW	12	11,324,008 (GRCm39)	missense	probably damaging	1.00
R5372:Smc6	UTSW	12	11,332,431 (GRCm39)	missense	probably damaging	1.00
R5412:Smc6	UTSW	12	11,335,400 (GRCm39)	missense	possibly damaging	0.88
R5523:Smc6	UTSW	12	11,341,540 (GRCm39)	missense	probably benign	0.31
R5643:Smc6	UTSW	12	11,339,995 (GRCm39)	missense	probably benign	0.18
R5644:Smc6	UTSW	12	11,339,995 (GRCm39)	missense	probably benign	0.18
R5782:Smc6	UTSW	12	11,340,835 (GRCm39)	missense	probably damaging	1.00
R6027:Smc6	UTSW	12	11,356,179 (GRCm39)	missense	probably benign	0.04
R6083:Smc6	UTSW	12	11,326,354 (GRCm39)	missense	possibly damaging	0.95
R6344:Smc6	UTSW	12	11,347,107 (GRCm39)	intron	probably benign
R6374:Smc6	UTSW	12	11,355,874 (GRCm39)	splice site	probably null
R6430:Smc6	UTSW	12	11,359,235 (GRCm39)	missense	probably benign	0.00
R6539:Smc6	UTSW	12	11,347,011 (GRCm39)	splice site	probably null
R6767:Smc6	UTSW	12	11,321,821 (GRCm39)	missense	possibly damaging	0.93
R7042:Smc6	UTSW	12	11,359,301 (GRCm39)	missense	probably damaging	1.00
R7128:Smc6	UTSW	12	11,351,632 (GRCm39)	missense	probably damaging	1.00
R7477:Smc6	UTSW	12	11,321,808 (GRCm39)	missense	probably benign
R7698:Smc6	UTSW	12	11,333,141 (GRCm39)	missense	possibly damaging	0.92
R7832:Smc6	UTSW	12	11,367,844 (GRCm39)	missense	probably benign	0.28
R7863:Smc6	UTSW	12	11,339,130 (GRCm39)	missense	probably benign	0.00
R8192:Smc6	UTSW	12	11,349,336 (GRCm39)	missense	probably benign	0.01
R8229:Smc6	UTSW	12	11,341,673 (GRCm39)	missense	probably benign	0.25
R8289:Smc6	UTSW	12	11,324,052 (GRCm39)	missense	probably benign	0.41
R9233:Smc6	UTSW	12	11,359,291 (GRCm39)	missense	probably benign	0.15
R9596:Smc6	UTSW	12	11,345,045 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- TCTTCAGAAGCGTTAGGCGGATAGC -3'
(R):5'- AAAGCCCACTCGCAGTAACTGTGC -3'

Sequencing Primer
(F):5'- CGTTAGGCGGATAGCTTAGGG -3'
(R):5'- CTGTTAAACATGATGCTTGCTGAC -3'

Posted On

2014-04-13