Mutagenetix > Incidental Mutation

Incidental Mutation 'R8711:Smc5'

669613

Institutional Source

Beutler Lab

Gene Symbol

Smc5

Ensembl Gene

ENSMUSG00000024943

Gene Name

structural maintenance of chromosomes 5

Synonyms

Smc5l1

MMRRC Submission

068565-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8711 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

23183815-23251261 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 23243058 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 118 (C118S)

Ref Sequence

ENSEMBL: ENSMUSP00000084837 (fasta)

Gene Model

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

AlphaFold

Q8CG46

Predicted Effect

probably damaging
Transcript: ENSMUST00000087556
AA Change: C118S

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000084837
Gene: ENSMUSG00000024943
AA Change: C118S

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: C118S

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000226111
AA Change: C42S

PolyPhen 2 Score 0.776 (Sensitivity: 0.85; Specificity: 0.92)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

99% (70/71)

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadat	T	A	8: 60,969,120 (GRCm39)	S122T	probably benign	Het
Abcb11	G	A	2: 69,095,856 (GRCm39)	T828I	probably damaging	Het
Atp5f1b	T	A	10: 127,921,369 (GRCm39)	N222K	probably damaging	Het
C1qbp	T	C	11: 70,869,313 (GRCm39)	T211A	probably benign	Het
Ccdc85a	A	T	11: 28,384,146 (GRCm39)	S410T	possibly damaging	Het
Chd4	T	A	6: 125,100,485 (GRCm39)		probably benign	Het
Col10a1	G	T	10: 34,270,824 (GRCm39)	K265N	probably damaging	Het
Cyp2j5	A	T	4: 96,529,660 (GRCm39)	M237K	possibly damaging	Het
Cyp4f40	T	C	17: 32,894,962 (GRCm39)		probably benign	Het
Cytip	A	T	2: 58,041,135 (GRCm39)	F90L	probably damaging	Het
Dnah7b	A	G	1: 46,214,598 (GRCm39)	D1121G	probably damaging	Het
Dohh	G	T	10: 81,221,859 (GRCm39)	E84D	probably benign	Het
Efcab3	A	G	11: 104,743,371 (GRCm39)	I2187V	probably benign	Het
Eif1ad19	T	A	12: 87,740,130 (GRCm39)	D143V	unknown	Het
Eif4g2	T	C	7: 110,673,127 (GRCm39)	Y855C	probably damaging	Het
Ell	T	A	8: 71,034,331 (GRCm39)		probably benign	Het
Ermap	T	C	4: 119,044,355 (GRCm39)	Y147C	probably damaging	Het
Fasn	T	C	11: 120,709,944 (GRCm39)	D371G	possibly damaging	Het
Fat2	A	G	11: 55,159,129 (GRCm39)	S3348P	probably benign	Het
Fhad1	T	A	4: 141,684,924 (GRCm39)	N472Y	probably benign	Het
Flad1	A	G	3: 89,316,415 (GRCm39)	V49A	probably damaging	Het
Fpr-rs3	T	C	17: 20,844,554 (GRCm39)	T196A	probably benign	Het
Fsip2	A	G	2: 82,815,246 (GRCm39)	N3660D	possibly damaging	Het
Gabrp	T	A	11: 33,505,023 (GRCm39)	L259F	probably damaging	Het
Gm16686	A	T	4: 88,673,473 (GRCm39)	W119R	unknown	Het
Gng2	C	T	14: 19,941,438 (GRCm39)	M1I	probably null	Het
Hmgxb3	T	C	18: 61,290,721 (GRCm39)	N384S	probably benign	Het
Ibtk	T	C	9: 85,606,208 (GRCm39)	I440V	probably benign	Het
Il11ra1	A	G	4: 41,767,539 (GRCm39)	D297G	probably damaging	Het
Irf2bpl	T	C	12: 86,928,496 (GRCm39)	I726V	probably benign	Het
Klk1b5	A	G	7: 43,867,996 (GRCm39)	N56S	probably benign	Het
Laptm4b	T	A	15: 34,277,648 (GRCm39)	V193E	probably damaging	Het
Lrrc37a	A	T	11: 103,388,350 (GRCm39)	C2358*	probably null	Het
Ltbp2	C	T	12: 84,900,515 (GRCm39)	S269N	probably benign	Het
Morc2a	T	G	11: 3,630,013 (GRCm39)	Y450D	probably damaging	Het
Mycbp2	A	T	14: 103,407,430 (GRCm39)	I2740K	probably benign	Het
Naif1	T	A	2: 32,344,848 (GRCm39)	V184E	probably damaging	Het
Neurl1b	T	C	17: 26,660,747 (GRCm39)	V540A	probably damaging	Het
Nt5c1b	T	A	12: 10,431,450 (GRCm39)	F451Y	probably damaging	Het
Obox3	A	G	7: 15,360,148 (GRCm39)	S174P	probably benign	Het
Obscn	T	C	11: 58,951,894 (GRCm39)	E3953G	probably damaging	Het
Or4a74	A	C	2: 89,440,291 (GRCm39)	S52A	probably benign	Het
Or4p19	A	T	2: 88,242,595 (GRCm39)	C136S	probably damaging	Het
Pkd1l1	G	A	11: 8,815,550 (GRCm39)	H1904Y		Het
Plec	C	T	15: 76,059,531 (GRCm39)	D3469N	probably benign	Het
Polr1b	A	G	2: 128,943,064 (GRCm39)	T20A	probably damaging	Het
Ppp1r16b	G	A	2: 158,603,286 (GRCm39)	E404K	possibly damaging	Het
Prkce	T	A	17: 86,795,625 (GRCm39)	N287K	probably damaging	Het
Rchy1	C	A	5: 92,105,397 (GRCm39)	C108F	probably damaging	Het
Scpppq1	G	A	5: 104,219,956 (GRCm39)	T78I	unknown	Het
Sema6d	A	G	2: 124,502,232 (GRCm39)	Y572C	possibly damaging	Het
Sh3rf1	T	A	8: 61,783,030 (GRCm39)	I248K	probably damaging	Het
Sin3b	T	C	8: 73,450,026 (GRCm39)	L30P	probably damaging	Het
Slc25a47	G	A	12: 108,820,313 (GRCm39)	G106S	probably damaging	Het
Slc43a2	A	C	11: 75,457,879 (GRCm39)	M385L	probably benign	Het
Slc43a3	A	G	2: 84,768,671 (GRCm39)	T97A	probably damaging	Het
Slc9b2	T	A	3: 135,030,351 (GRCm39)	S223T	probably benign	Het
Smpdl3b	T	C	4: 132,472,491 (GRCm39)	D94G	probably damaging	Het
Spred3	A	G	7: 28,866,086 (GRCm39)	V71A	possibly damaging	Het
Srsf5	T	A	12: 80,994,328 (GRCm39)	S86T	possibly damaging	Het
Sycp2	A	G	2: 177,990,088 (GRCm39)	V1386A	probably benign	Het
Syne2	T	C	12: 76,104,258 (GRCm39)	L743P	probably damaging	Het
Synj1	A	G	16: 90,806,971 (GRCm39)	V62A	probably damaging	Het
Tbc1d9b	T	C	11: 50,047,578 (GRCm39)	L637P	probably damaging	Het
Tcf12	T	G	9: 71,757,097 (GRCm39)	S697R	possibly damaging	Het
Tnfrsf11b	T	A	15: 54,123,508 (GRCm39)	Y31F	possibly damaging	Het
Trav5n-4	T	C	14: 53,550,362 (GRCm39)	M1T	probably null	Het
Trbv13-2	A	G	6: 41,098,716 (GRCm39)	E97G	probably benign	Het
Trpa1	G	A	1: 14,980,998 (GRCm39)	P135S	probably damaging	Het
Ugt1a6a	A	C	1: 88,066,590 (GRCm39)	D132A	possibly damaging	Het
Vmn2r8	A	T	5: 108,945,962 (GRCm39)	D548E	possibly damaging	Het
Zbtb39	A	T	10: 127,578,815 (GRCm39)	D463V	probably damaging	Het
Zc3h12c	C	T	9: 52,037,858 (GRCm39)		probably benign	Het
Zfp952	C	T	17: 33,222,004 (GRCm39)	P161L	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
R6750:Smc5	UTSW	19	23,220,004 (GRCm39)	missense	probably damaging	1.00
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
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'- AGGTCAAGGACTTAAGTACATCAGG -3'
(R):5'- AAGAGTTGAGGGACTTGGCC -3'

Sequencing Primer
(F):5'- TGCTGGAATTACGAAGTGTACCAC -3'
(R):5'- AGGGACTTGGCCTGTACATTAATG -3'

Posted On

2021-04-30