Mutagenetix > Incidental Mutation

Incidental Mutation 'R6750:Smc5'

530742

Institutional Source

Beutler Lab

Gene Symbol

Smc5

Ensembl Gene

ENSMUSG00000024943

Gene Name

structural maintenance of chromosomes 5

Synonyms

Smc5l1

MMRRC Submission

044867-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6750 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

23183815-23251261 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 23220004 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 411 (L411P)

Ref Sequence

ENSEMBL: ENSMUSP00000153420 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000087556] [ENSMUST00000223934] [ENSMUST00000226111]

AlphaFold

Q8CG46

Predicted Effect

probably damaging
Transcript: ENSMUST00000087556
AA Change: L487P

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

SMART Domains

Protein: ENSMUSP00000084837
Gene: ENSMUSG00000024943
AA Change: L487P

Domain	Start	End	E-Value	Type
Pfam:SMC_N	52	1057	9.2e-19	PFAM
Pfam:AAA_23	55	456	1.2e-9	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000223934
AA Change: L487P

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000226111
AA Change: L411P

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

Meta Mutation Damage Score

0.8495

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.6%
20x: 92.7%

Validation Efficiency

100% (75/75)

MGI Phenotype

PHENOTYPE: Homozygous knockout in embryonic stem cells causes abnormal mitosis, increased apoptosis and a shift from pluripotency to differentiation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adal	A	T	2: 120,973,130 (GRCm39)	L62F	probably damaging	Het
Akap13	C	T	7: 75,389,206 (GRCm39)	P2375S	probably benign	Het
Apob	T	A	12: 8,047,853 (GRCm39)	L931Q	probably damaging	Het
Arcn1	A	G	9: 44,661,691 (GRCm39)	V391A	possibly damaging	Het
Ccdc162	A	T	10: 41,437,222 (GRCm39)	I1729N	possibly damaging	Het
Cd24a	T	C	10: 43,458,721 (GRCm39)	L86P	unknown	Het
Cdcp3	T	A	7: 130,889,974 (GRCm39)		probably benign	Het
Churc1	C	A	12: 76,822,405 (GRCm39)	H71Q	probably damaging	Het
Clcn3	A	G	8: 61,367,809 (GRCm39)	L780P	possibly damaging	Het
Cldn17	C	T	16: 88,303,195 (GRCm39)	G178E	possibly damaging	Het
Cmah	A	G	13: 24,648,235 (GRCm39)	Y345C	probably damaging	Het
Cntnap5b	C	T	1: 100,202,224 (GRCm39)	S357L	probably damaging	Het
Col6a6	A	G	9: 105,660,879 (GRCm39)	I410T	probably damaging	Het
Crmp1	T	C	5: 37,422,666 (GRCm39)		probably null	Het
Csmd2	A	C	4: 128,091,018 (GRCm39)	N186H	possibly damaging	Het
Cyp1a1	A	T	9: 57,607,539 (GRCm39)	M56L	probably benign	Het
D2hgdh	G	C	1: 93,754,129 (GRCm39)	R56P	probably benign	Het
Dapk2	A	G	9: 66,128,034 (GRCm39)	E104G	probably damaging	Het
Dld	T	C	12: 31,382,213 (GRCm39)	N498S	probably benign	Het
Dyrk4	G	T	6: 126,875,918 (GRCm39)	Q106K	probably benign	Het
Eif2b4	T	C	5: 31,347,304 (GRCm39)	I333V	probably damaging	Het
F5	A	G	1: 164,021,076 (GRCm39)	T1184A	possibly damaging	Het
Fbxl6	C	T	15: 76,422,612 (GRCm39)	G102D	probably damaging	Het
Foxa1	C	T	12: 57,589,396 (GRCm39)	G275R	probably benign	Het
Fryl	A	G	5: 73,179,575 (GRCm39)	I2944T	probably damaging	Het
Gna15	T	C	10: 81,350,117 (GRCm39)	D95G	probably benign	Het
Greb1	T	A	12: 16,738,584 (GRCm39)	M1460L	probably benign	Het
Herc1	TCCC	TCC	9: 66,408,470 (GRCm39)		probably null	Het
Herc2	T	C	7: 55,747,195 (GRCm39)	I444T	probably damaging	Het
Ifngr1	T	A	10: 19,485,099 (GRCm39)	M366K	probably benign	Het
Krt27	C	T	11: 99,239,806 (GRCm39)	E253K	probably damaging	Het
Mical2	C	T	7: 111,981,046 (GRCm39)	T406I	probably damaging	Het
Mocs2	T	G	13: 114,962,784 (GRCm39)	D156E	probably damaging	Het
Mprip	A	T	11: 59,586,957 (GRCm39)	K43N	probably damaging	Het
Myo5b	A	T	18: 74,750,106 (GRCm39)	T190S	possibly damaging	Het
Naa25	C	T	5: 121,546,372 (GRCm39)	T86M	probably damaging	Het
Ncam1	T	C	9: 49,478,639 (GRCm39)	D163G	probably damaging	Het
Nlrp4f	A	T	13: 65,329,468 (GRCm39)	Y908*	probably null	Het
Nlrp9b	T	A	7: 19,757,159 (GRCm39)	L132*	probably null	Het
Nrg1	A	C	8: 32,308,124 (GRCm39)	S679A	probably damaging	Het
Or1j1	C	A	2: 36,702,954 (GRCm39)	R50M	possibly damaging	Het
Or52p1	C	T	7: 104,267,320 (GRCm39)	R145C	probably damaging	Het
Paqr9	A	T	9: 95,443,050 (GRCm39)	T347S	probably damaging	Het
Pcdhb21	T	C	18: 37,647,501 (GRCm39)	L210P	probably damaging	Het
Pdzd7	T	G	19: 45,016,187 (GRCm39)	D978A	probably benign	Het
Phf8-ps	A	T	17: 33,285,372 (GRCm39)	S477T	possibly damaging	Het
Pkd1l1	A	T	11: 8,923,217 (GRCm39)	S17T	unknown	Het
Plcz1	T	C	6: 139,974,164 (GRCm39)	K93E	possibly damaging	Het
Pom121l2	G	C	13: 22,166,107 (GRCm39)	R126P	probably damaging	Het
Prkg1	C	T	19: 31,741,961 (GRCm39)	E88K	probably benign	Het
Psme4	A	T	11: 30,803,203 (GRCm39)	D15V	probably damaging	Het
Ptprf	A	G	4: 118,088,928 (GRCm39)	V625A	probably benign	Het
Rab27a	G	A	9: 72,992,290 (GRCm39)	S106N	probably damaging	Het
Rasa4	A	G	5: 136,129,802 (GRCm39)	T261A	probably benign	Het
Sardh	T	C	2: 27,118,269 (GRCm39)	D487G	probably benign	Het
Sec16a	A	G	2: 26,330,030 (GRCm39)	Y662H	probably benign	Het
Sema3d	T	A	5: 12,635,067 (GRCm39)	L711*	probably null	Het
Septin14	T	A	5: 129,773,181 (GRCm39)	Y152F	probably damaging	Het
Spata31e5	C	A	1: 28,816,495 (GRCm39)	E512D	probably damaging	Het
Spg7	T	A	8: 123,800,650 (GRCm39)	V39E	probably damaging	Het
Tas2r117	A	G	6: 132,779,817 (GRCm39)		probably benign	Het
Tle1	A	T	4: 72,040,687 (GRCm39)	I631N	probably damaging	Het
Tmed3	T	A	9: 89,581,843 (GRCm39)	S207C	probably damaging	Het
Tmem59l	G	A	8: 70,939,022 (GRCm39)	P51S	probably benign	Het
Trpc3	A	G	3: 36,678,542 (GRCm39)	Y848H	probably damaging	Het
Tsen2	T	C	6: 115,526,881 (GRCm39)	F66S	probably damaging	Het
Ttll5	T	A	12: 86,003,384 (GRCm39)	S216R	probably damaging	Het
Usp22	A	T	11: 61,048,042 (GRCm39)	V426E	probably damaging	Het
Vmn2r76	T	C	7: 85,875,114 (GRCm39)	N621S	probably damaging	Het
Wdr75	A	G	1: 45,856,539 (GRCm39)	T521A	probably damaging	Het
Wrnip1	T	A	13: 32,986,739 (GRCm39)	D173E	probably damaging	Het
Zfp317	G	A	9: 19,559,100 (GRCm39)	G438D	probably damaging	Het
Zscan10	T	A	17: 23,826,164 (GRCm39)	S109T	possibly damaging	Het

Other mutations in Smc5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00569:Smc5	APN	19	23,213,329 (GRCm39)	missense	probably damaging	1.00
IGL01070:Smc5	APN	19	23,208,965 (GRCm39)	missense	possibly damaging	0.86
IGL01315:Smc5	APN	19	23,208,968 (GRCm39)	missense	probably benign
IGL01879:Smc5	APN	19	23,205,548 (GRCm39)	missense	probably damaging	0.97
IGL01902:Smc5	APN	19	23,237,132 (GRCm39)	missense	possibly damaging	0.85
IGL02016:Smc5	APN	19	23,251,076 (GRCm39)	missense	probably benign	0.00
IGL02186:Smc5	APN	19	23,209,223 (GRCm39)	missense	probably damaging	1.00
IGL02383:Smc5	APN	19	23,191,996 (GRCm39)	splice site	probably benign
IGL02447:Smc5	APN	19	23,234,856 (GRCm39)	missense	probably benign	0.01
IGL02534:Smc5	APN	19	23,205,536 (GRCm39)	critical splice donor site	probably null
IGL02834:Smc5	APN	19	23,234,968 (GRCm39)	missense	probably benign	0.30
IGL03290:Smc5	APN	19	23,251,022 (GRCm39)	missense	probably benign	0.19
R0722:Smc5	UTSW	19	23,186,291 (GRCm39)	missense	probably damaging	0.99
R0893:Smc5	UTSW	19	23,241,017 (GRCm39)	missense	possibly damaging	0.67
R0970:Smc5	UTSW	19	23,216,362 (GRCm39)	missense	probably damaging	1.00
R1281:Smc5	UTSW	19	23,213,247 (GRCm39)	missense	probably benign
R1368:Smc5	UTSW	19	23,187,807 (GRCm39)	missense	probably damaging	1.00
R2092:Smc5	UTSW	19	23,216,263 (GRCm39)	missense	probably benign
R3721:Smc5	UTSW	19	23,187,856 (GRCm39)	missense	probably benign	0.21
R4382:Smc5	UTSW	19	23,246,210 (GRCm39)	missense	probably benign	0.39
R4735:Smc5	UTSW	19	23,220,069 (GRCm39)	missense	probably benign
R4936:Smc5	UTSW	19	23,211,367 (GRCm39)	missense	probably damaging	1.00
R5306:Smc5	UTSW	19	23,237,009 (GRCm39)	critical splice donor site	probably null
R5754:Smc5	UTSW	19	23,221,467 (GRCm39)	missense	possibly damaging	0.92
R6175:Smc5	UTSW	19	23,191,534 (GRCm39)	missense	possibly damaging	0.60
R6313:Smc5	UTSW	19	23,186,312 (GRCm39)	nonsense	probably null
R6527:Smc5	UTSW	19	23,205,554 (GRCm39)	missense	probably benign	0.00
R6611:Smc5	UTSW	19	23,206,283 (GRCm39)	missense	probably benign	0.13
R6801:Smc5	UTSW	19	23,192,010 (GRCm39)	missense	probably benign	0.34
R6821:Smc5	UTSW	19	23,220,151 (GRCm39)	missense	probably benign	0.20
R7002:Smc5	UTSW	19	23,209,247 (GRCm39)	missense	probably benign	0.00
R7198:Smc5	UTSW	19	23,237,064 (GRCm39)	nonsense	probably null
R7386:Smc5	UTSW	19	23,192,539 (GRCm39)	missense	possibly damaging	0.59
R7439:Smc5	UTSW	19	23,220,064 (GRCm39)	missense	probably damaging	0.97
R7596:Smc5	UTSW	19	23,191,533 (GRCm39)	missense	probably damaging	0.99
R7666:Smc5	UTSW	19	23,206,381 (GRCm39)	missense	probably benign	0.15
R7760:Smc5	UTSW	19	23,213,254 (GRCm39)	missense	probably benign	0.01
R7990:Smc5	UTSW	19	23,213,246 (GRCm39)	missense	probably benign	0.01
R8255:Smc5	UTSW	19	23,186,290 (GRCm39)	missense
R8359:Smc5	UTSW	19	23,211,443 (GRCm39)	missense	possibly damaging	0.49
R8473:Smc5	UTSW	19	23,221,446 (GRCm39)	missense	probably benign	0.02
R8711:Smc5	UTSW	19	23,243,058 (GRCm39)	missense	probably damaging	0.98
R8815:Smc5	UTSW	19	23,221,422 (GRCm39)	missense	probably damaging	1.00
R8885:Smc5	UTSW	19	23,191,234 (GRCm39)	missense	probably damaging	0.99
R8940:Smc5	UTSW	19	23,237,126 (GRCm39)	missense	probably benign	0.00
R9642:Smc5	UTSW	19	23,238,752 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- CCCTTTAGAAAGCTCATGCATGG -3'
(R):5'- GAAGAAACCTGTCATGCCCCTC -3'

Sequencing Primer
(F):5'- AGCTCATGCATGGATTCAGC -3'
(R):5'- CTGGAACTCACTTTGTAGACCAGG -3'

Posted On

2018-08-01