Mutagenetix > Incidental Mutation

Incidental Mutation 'R7051:Smc4'

547565

Institutional Source

Beutler Lab

Gene Symbol

Smc4

Ensembl Gene

ENSMUSG00000034349

Gene Name

structural maintenance of chromosomes 4

Synonyms

Smc4l1, 2500002A22Rik

MMRRC Submission

045148-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.971) question?

Stock #

R7051 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

68912071-68941956 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 68934835 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tryptophan to Arginine at position 650 (W650R)

Ref Sequence

ENSEMBL: ENSMUSP00000103433 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000042901] [ENSMUST00000107803] [ENSMUST00000148385] [ENSMUST00000195525]

AlphaFold

Q8CG47

Predicted Effect

probably damaging
Transcript: ENSMUST00000042901
AA Change: W675R

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

SMART Domains

Protein: ENSMUSP00000047872
Gene: ENSMUSG00000034349
AA Change: W675R

Domain	Start	End	E-Value	Type
PDB:1W1W\|D	89	238	1e-17	PDB
Blast:AAA	104	238	3e-6	BLAST
low complexity region	408	427	N/A	INTRINSIC
low complexity region	447	460	N/A	INTRINSIC
low complexity region	473	482	N/A	INTRINSIC
low complexity region	545	567	N/A	INTRINSIC
SMC_hinge	611	726	1.12e-31	SMART
low complexity region	870	881	N/A	INTRINSIC
low complexity region	942	953	N/A	INTRINSIC
Blast:AAA	1102	1276	5e-26	BLAST
PDB:3KTA\|D	1125	1276	3e-30	PDB
SCOP:d1e69a_	1188	1263	3e-5	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000107803
AA Change: W650R

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

SMART Domains

Protein: ENSMUSP00000103433
Gene: ENSMUSG00000034349
AA Change: W650R

Domain	Start	End	E-Value	Type
Pfam:AAA_23	59	329	1.3e-12	PFAM
Pfam:AAA_21	81	199	5.2e-7	PFAM
coiled coil region	369	482	N/A	INTRINSIC
coiled coil region	511	563	N/A	INTRINSIC
SMC_hinge	586	701	8.6e-36	SMART
Pfam:SMC_N	738	1247	1.1e-35	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000148385

Predicted Effect

probably benign
Transcript: ENSMUST00000149174

Predicted Effect

probably benign
Transcript: ENSMUST00000195525

Meta Mutation Damage Score

0.5541

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

95% (80/84)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the 'structural maintenance of chromosomes' (SMC) gene family. Members of this gene family play a role in two changes in chromosome structure during mitotic segregation of chromosomes- chromosome condensation and sister chromatid cohesion. The protein encoded by this gene is likely a subunit of the 13S condensin complex, which is involved in chromosome condensation. A pseudogene related to this gene is located on chromosome 2. [provided by RefSeq, Jun 2016]

Allele List at MGI

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5930422O12Rik	C	T	8: 33,919,201 (GRCm39)	S7L	unknown	Het
Aggf1	T	C	13: 95,488,125 (GRCm39)	K674R	possibly damaging	Het
Ampd1	T	C	3: 102,997,389 (GRCm39)	F264L	probably damaging	Het
Ankle1	A	T	8: 71,860,387 (GRCm39)	S302C	probably damaging	Het
Ankrd17	G	A	5: 90,514,310 (GRCm39)		probably benign	Het
Arhgap18	T	A	10: 26,725,917 (GRCm39)	N47K	possibly damaging	Het
Atp5pb	T	C	3: 105,851,083 (GRCm39)	N205D	probably benign	Het
Atp8b3	C	T	10: 80,355,858 (GRCm39)	E1285K	probably benign	Het
Atp8b3	C	A	10: 80,365,552 (GRCm39)	V401L	probably damaging	Het
Cacna1a	G	A	8: 85,356,544 (GRCm39)	R1929Q	possibly damaging	Het
Cadm2	C	T	16: 66,679,767 (GRCm39)	S22N	possibly damaging	Het
Ccdc177	C	T	12: 80,805,927 (GRCm39)	V116M	probably damaging	Het
Cdhr18	A	G	14: 13,828,486 (GRCm38)	V758A		Het
Cdkl2	A	T	5: 92,181,084 (GRCm39)	I185N	probably damaging	Het
Cfhr2	T	A	1: 139,738,716 (GRCm39)	I282L	probably benign	Het
Clns1a	T	A	7: 97,361,824 (GRCm39)		probably null	Het
Commd2	A	T	3: 57,554,107 (GRCm39)	I198N	probably damaging	Het
Creb3l2	C	T	6: 37,313,200 (GRCm39)	V365I	possibly damaging	Het
Dcaf6	A	T	1: 165,251,886 (GRCm39)	N79K	possibly damaging	Het
Dlg5	T	C	14: 24,196,263 (GRCm39)	N1622D	possibly damaging	Het
Dock7	C	T	4: 98,834,969 (GRCm39)	R1802H	probably damaging	Het
Dpy19l2	T	C	9: 24,495,789 (GRCm39)	K643R	probably benign	Het
Dscam	G	A	16: 96,620,986 (GRCm39)	T574M	probably benign	Het
Fam209	A	G	2: 172,315,969 (GRCm39)	T115A	probably damaging	Het
Fastkd5	C	T	2: 130,456,337 (GRCm39)	C751Y	probably damaging	Het
Fat3	C	A	9: 16,289,123 (GRCm39)	L133F	probably damaging	Het
Fcsk	A	T	8: 111,616,971 (GRCm39)	I393N	probably damaging	Het
Frmd6	T	C	12: 70,944,170 (GRCm39)	V516A	possibly damaging	Het
Fry	G	A	5: 150,318,634 (GRCm39)	D955N	possibly damaging	Het
Gm7298	T	C	6: 121,751,993 (GRCm39)		probably null	Het
Golga7b	T	A	19: 42,256,899 (GRCm39)	*168R	probably null	Het
Golim4	T	A	3: 75,800,309 (GRCm39)	Q395L	probably benign	Het
Gxylt2	T	A	6: 100,781,537 (GRCm39)	L404*	probably null	Het
H1f4	A	G	13: 23,806,422 (GRCm39)	V20A	probably benign	Het
Ighmbp2	G	T	19: 3,311,462 (GRCm39)	S984R	probably damaging	Het
Irf8	C	T	8: 121,466,581 (GRCm39)	R9W	probably damaging	Het
Itga4	T	C	2: 79,148,470 (GRCm39)	V788A	possibly damaging	Het
Kifap3	G	A	1: 163,621,649 (GRCm39)	R99H	probably damaging	Het
Kiss1r	T	C	10: 79,754,688 (GRCm39)	S61P	probably damaging	Het
Krtap6-1	A	T	16: 88,828,606 (GRCm39)	M1L	unknown	Het
Large2	A	T	2: 92,197,367 (GRCm39)	M411K	probably damaging	Het
Lcor	A	G	19: 41,574,191 (GRCm39)	D982G	probably benign	Het
Lingo1	A	G	9: 56,527,467 (GRCm39)	V374A	probably benign	Het
Lrch1	A	G	14: 75,022,962 (GRCm39)	V637A	probably damaging	Het
Lyar	T	C	5: 38,382,024 (GRCm39)	V2A	probably damaging	Het
Nell1	C	T	7: 50,098,592 (GRCm39)	S298L	unknown	Het
Ogfod3	T	A	11: 121,086,031 (GRCm39)	I188F	probably damaging	Het
Opa3	C	A	7: 18,978,961 (GRCm39)	A142E	possibly damaging	Het
Or5b123	T	A	19: 13,596,769 (GRCm39)	M81K	possibly damaging	Het
Or5k1	T	C	16: 58,617,538 (GRCm39)	T224A	probably benign	Het
Pald1	T	C	10: 61,159,125 (GRCm39)	R769G	probably benign	Het
Pappa2	T	A	1: 158,784,753 (GRCm39)	T86S	unknown	Het
Papss1	T	C	3: 131,307,811 (GRCm39)	Y266H	probably damaging	Het
Pcdhga7	C	A	18: 37,849,994 (GRCm39)	A667D	probably damaging	Het
Pcsk5	T	A	19: 17,411,095 (GRCm39)	T1766S	probably benign	Het
Pds5b	T	A	5: 150,717,747 (GRCm39)	N1129K	possibly damaging	Het
Pop7	T	C	5: 137,499,952 (GRCm39)	N127S	probably damaging	Het
Ppfibp2	A	G	7: 107,316,925 (GRCm39)	E300G	probably damaging	Het
Ppp4r3b	A	G	11: 29,132,507 (GRCm39)	K87E	probably damaging	Het
Psmd3	T	A	11: 98,573,659 (GRCm39)	M35K	possibly damaging	Het
Pus7	A	G	5: 23,980,677 (GRCm39)	V191A	probably damaging	Het
Rptor	C	T	11: 119,765,012 (GRCm39)		probably benign	Het
Sacs	A	G	14: 61,446,377 (GRCm39)	M2808V	probably benign	Het
Scube3	G	A	17: 28,386,573 (GRCm39)	V831I	probably benign	Het
Sin3a	A	T	9: 57,011,218 (GRCm39)	N492Y	probably damaging	Het
Slc12a3	A	G	8: 95,092,572 (GRCm39)	T998A	probably damaging	Het
Slc4a1	T	C	11: 102,247,084 (GRCm39)	N501S	probably benign	Het
Sltm	G	A	9: 70,466,348 (GRCm39)	G94R	probably damaging	Het
Smg7	A	G	1: 152,724,601 (GRCm39)	S527P	probably damaging	Het
Tcf20	T	C	15: 82,740,279 (GRCm39)	N391D	probably damaging	Het
Tiam2	G	A	17: 3,498,758 (GRCm39)	V845M	probably damaging	Het
Tln2	A	G	9: 67,253,699 (GRCm39)	F793L	probably benign	Het
Uckl1	T	C	2: 181,216,037 (GRCm39)	I193V	probably damaging	Het
Ugt1a5	A	G	1: 88,094,077 (GRCm39)	M102V	probably benign	Het
Usp38	G	A	8: 81,727,750 (GRCm39)	P328S	possibly damaging	Het
Vmn1r189	A	G	13: 22,286,285 (GRCm39)	V184A	possibly damaging	Het
Vps13d	C	A	4: 144,889,914 (GRCm39)	A597S	probably benign	Het
Wdr47	T	A	3: 108,525,840 (GRCm39)	L121Q	probably damaging	Het
Wiz	A	G	17: 32,580,507 (GRCm39)	S315P	probably damaging	Het
Zc3h13	T	C	14: 75,568,597 (GRCm39)	S1297P	probably damaging	Het
Zfp27	AATCCGCTTGTGCA	AA	7: 29,594,446 (GRCm39)		probably benign	Het

Other mutations in Smc4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00401:Smc4	APN	3	68,937,712 (GRCm39)	missense	probably damaging	0.98
IGL00542:Smc4	APN	3	68,935,771 (GRCm39)	splice site	probably benign
IGL01104:Smc4	APN	3	68,934,917 (GRCm39)	missense	possibly damaging	0.95
IGL01380:Smc4	APN	3	68,933,161 (GRCm39)	missense	probably damaging	1.00
IGL01397:Smc4	APN	3	68,938,877 (GRCm39)	missense	probably benign
IGL02441:Smc4	APN	3	68,913,544 (GRCm39)	missense	probably damaging	1.00
IGL02629:Smc4	APN	3	68,933,206 (GRCm39)	missense	probably damaging	0.96
IGL03220:Smc4	APN	3	68,916,875 (GRCm39)	missense	possibly damaging	0.67
pyrrhic	UTSW	3	68,934,835 (GRCm39)	missense	probably damaging	1.00
R0452:Smc4	UTSW	3	68,915,361 (GRCm39)	nonsense	probably null
R0523:Smc4	UTSW	3	68,933,221 (GRCm39)	missense	probably damaging	1.00
R0568:Smc4	UTSW	3	68,929,794 (GRCm39)	critical splice donor site	probably null
R0571:Smc4	UTSW	3	68,931,622 (GRCm39)	missense	probably damaging	1.00
R0602:Smc4	UTSW	3	68,916,871 (GRCm39)	missense	probably damaging	1.00
R0925:Smc4	UTSW	3	68,913,548 (GRCm39)	critical splice donor site	probably benign
R0963:Smc4	UTSW	3	68,933,259 (GRCm39)	missense	probably damaging	1.00
R1540:Smc4	UTSW	3	68,924,105 (GRCm39)	missense	probably damaging	1.00
R1755:Smc4	UTSW	3	68,941,441 (GRCm39)	missense	probably damaging	1.00
R1920:Smc4	UTSW	3	68,940,401 (GRCm39)	missense	probably damaging	1.00
R4226:Smc4	UTSW	3	68,938,800 (GRCm39)	missense	probably benign	0.01
R4510:Smc4	UTSW	3	68,923,980 (GRCm39)	splice site	probably null
R4511:Smc4	UTSW	3	68,923,980 (GRCm39)	splice site	probably null
R4899:Smc4	UTSW	3	68,939,144 (GRCm39)	missense	probably damaging	0.97
R4967:Smc4	UTSW	3	68,925,572 (GRCm39)	intron	probably benign
R5096:Smc4	UTSW	3	68,928,612 (GRCm39)	missense	probably damaging	1.00
R5101:Smc4	UTSW	3	68,935,845 (GRCm39)	missense	probably benign	0.00
R5588:Smc4	UTSW	3	68,933,190 (GRCm39)	missense	probably benign
R5631:Smc4	UTSW	3	68,937,645 (GRCm39)	missense	probably benign	0.16
R5633:Smc4	UTSW	3	68,915,443 (GRCm39)	missense	probably damaging	1.00
R6229:Smc4	UTSW	3	68,937,580 (GRCm39)	nonsense	probably null
R6300:Smc4	UTSW	3	68,935,224 (GRCm39)	missense	probably benign	0.00
R6554:Smc4	UTSW	3	68,936,848 (GRCm39)	missense	probably benign	0.00
R6596:Smc4	UTSW	3	68,933,226 (GRCm39)	missense	probably damaging	1.00
R6603:Smc4	UTSW	3	68,929,794 (GRCm39)	critical splice donor site	probably null
R6682:Smc4	UTSW	3	68,914,574 (GRCm39)	missense	probably damaging	0.98
R6727:Smc4	UTSW	3	68,924,105 (GRCm39)	missense	probably damaging	1.00
R6955:Smc4	UTSW	3	68,931,642 (GRCm39)	missense	possibly damaging	0.95
R7037:Smc4	UTSW	3	68,925,528 (GRCm39)	missense	possibly damaging	0.67
R7454:Smc4	UTSW	3	68,925,457 (GRCm39)	missense	probably benign
R7630:Smc4	UTSW	3	68,925,400 (GRCm39)	critical splice acceptor site	probably benign
R7632:Smc4	UTSW	3	68,925,400 (GRCm39)	critical splice acceptor site	probably benign
R7633:Smc4	UTSW	3	68,925,400 (GRCm39)	critical splice acceptor site	probably benign
R7773:Smc4	UTSW	3	68,923,496 (GRCm39)	missense	probably damaging	1.00
R7857:Smc4	UTSW	3	68,940,552 (GRCm39)	missense	possibly damaging	0.61
R8008:Smc4	UTSW	3	68,914,645 (GRCm39)	missense	probably damaging	0.99
R8398:Smc4	UTSW	3	68,933,184 (GRCm39)	missense	probably damaging	1.00
R8527:Smc4	UTSW	3	68,940,224 (GRCm39)	critical splice donor site	probably null
R8936:Smc4	UTSW	3	68,925,491 (GRCm39)	missense	probably benign	0.21
R8998:Smc4	UTSW	3	68,934,894 (GRCm39)	utr 3 prime	probably benign
R9267:Smc4	UTSW	3	68,941,786 (GRCm39)	missense	probably damaging	1.00
R9440:Smc4	UTSW	3	68,915,455 (GRCm39)	critical splice donor site	probably null
R9476:Smc4	UTSW	3	68,914,662 (GRCm39)	missense	probably damaging	1.00
R9510:Smc4	UTSW	3	68,914,662 (GRCm39)	missense	probably damaging	1.00
R9777:Smc4	UTSW	3	68,929,655 (GRCm39)	nonsense	probably null
X0063:Smc4	UTSW	3	68,925,436 (GRCm39)	missense	possibly damaging	0.47

Predicted Primers

PCR Primer
(F):5'- GATGTCCAATGCATTTCGAGG -3'
(R):5'- CAGCGTCTGTCTCTTTGGTACG -3'

Sequencing Primer
(F):5'- GTCCAATGCATTTCGAGGTTTTAAC -3'
(R):5'- TCTTTGGTACGCTACTCTTGTAG -3'

Posted On

2019-05-13