Mutagenetix > Incidental Mutations

Incidental Mutation 'R5633:Smc4'

439965

Institutional Source

Beutler Lab

Gene Symbol

Smc4

Ensembl Gene

ENSMUSG00000034349

Gene Name

structural maintenance of chromosomes 4

Synonyms

2500002A22Rik, Smc4l1

MMRRC Submission

043284-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.968) question?

Stock #

R5633 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

69004738-69034623 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 69008110 bp

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Lysine at position 165 (I165K)

Ref Sequence

ENSEMBL: ENSMUSP00000115033 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000042901] [ENSMUST00000107803] [ENSMUST00000107812] [ENSMUST00000136502] [ENSMUST00000148031] [ENSMUST00000148385] [ENSMUST00000154741] [ENSMUST00000169064] [ENSMUST00000195525]

Predicted Effect

probably damaging
Transcript: ENSMUST00000042901
AA Change: I165K

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

SMART Domains

Protein: ENSMUSP00000047872
Gene: ENSMUSG00000034349
AA Change: I165K

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

noncoding transcript
Transcript: ENSMUST00000083646

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000083672

Predicted Effect

probably damaging
Transcript: ENSMUST00000107803
AA Change: I140K

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

SMART Domains

Protein: ENSMUSP00000103433
Gene: ENSMUSG00000034349
AA Change: I140K

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: ENSMUST00000107812

SMART Domains

Protein: ENSMUSP00000103442
Gene: ENSMUSG00000027778

Domain	Start	End	E-Value	Type
WD40	4	41	1.43e0	SMART
Blast:WD40	46	93	4e-9	BLAST
WD40	95	134	9.38e-5	SMART
WD40	136	176	2.75e1	SMART
WD40	177	216	1.42e-4	SMART
WD40	219	256	1.56e-1	SMART
WD40	258	297	2.75e1	SMART
low complexity region	429	440	N/A	INTRINSIC
Blast:WD40	496	533	4e-18	BLAST
low complexity region	764	772	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136448

Predicted Effect

probably damaging
Transcript: ENSMUST00000136502
AA Change: I165K

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

SMART Domains

Protein: ENSMUSP00000115033
Gene: ENSMUSG00000034349
AA Change: I165K

Domain	Start	End	E-Value	Type
Pfam:SMC_N	81	303	1.2e-42	PFAM
Pfam:AAA_23	84	336	2.6e-16	PFAM
Pfam:AAA_21	106	227	1e-9	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000148031

SMART Domains

Protein: ENSMUSP00000122919
Gene: ENSMUSG00000027778

Domain	Start	End	E-Value	Type
WD40	4	41	1.43e0	SMART
Blast:WD40	46	93	3e-10	BLAST
WD40	95	134	9.38e-5	SMART
Blast:WD40	136	159	1e-8	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000148385

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152502

Predicted Effect

probably benign
Transcript: ENSMUST00000154741

SMART Domains

Protein: ENSMUSP00000118406
Gene: ENSMUSG00000027778

Domain	Start	End	E-Value	Type
WD40	4	41	1.43e0	SMART
Blast:WD40	46	93	9e-10	BLAST
WD40	95	134	9.38e-5	SMART
WD40	136	176	2.75e1	SMART
WD40	177	209	2.12e2	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000169064

SMART Domains

Protein: ENSMUSP00000133263
Gene: ENSMUSG00000027778

Domain	Start	End	E-Value	Type
WD40	4	41	1.43e0	SMART
Blast:WD40	46	93	4e-9	BLAST
WD40	95	134	9.38e-5	SMART
WD40	136	176	2.75e1	SMART
WD40	177	216	1.42e-4	SMART
WD40	219	256	1.56e-1	SMART
WD40	258	297	2.75e1	SMART
low complexity region	429	440	N/A	INTRINSIC
Blast:WD40	496	533	4e-18	BLAST
low complexity region	764	772	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176135

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000192467

Predicted Effect

probably benign
Transcript: ENSMUST00000195525

Meta Mutation Damage Score

0.6760

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.6%
20x: 96.0%

Validation Efficiency

98% (55/56)

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: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl4	T	A	4: 144,618,028	C125S	probably benign	Het
Abcb8	T	C	5: 24,403,109	L382P	probably damaging	Het
Acot3	A	G	12: 84,058,950		probably null	Het
Acsl6	A	T	11: 54,337,189	Q345L	probably benign	Het
Adcy8	A	G	15: 64,699,285	S1170P	probably damaging	Het
Ankrd28	T	G	14: 31,735,065	D182A	probably damaging	Het
B3galt5	A	T	16: 96,315,509	H114L	probably benign	Het
BC053393	C	T	11: 46,574,606	S9L	unknown	Het
Bcas2	T	A	3: 103,178,424	Y207*	probably null	Het
Best1	A	G	19: 9,992,103	L197P	probably benign	Het
Chil6	C	A	3: 106,388,752	C389F	probably damaging	Het
Chrna4	T	C	2: 181,029,460	T168A	probably damaging	Het
Ckmt1	C	G	2: 121,363,629		probably benign	Het
Dhcr7	T	C	7: 143,847,423	L441P	probably damaging	Het
Dmtn	T	C	14: 70,604,979	M365V	probably benign	Het
Dmxl1	T	A	18: 49,877,697	S974T	probably damaging	Het
Dnajb13	T	C	7: 100,507,419	D150G	probably benign	Het
Eef2k	C	A	7: 120,873,290		probably benign	Het
Elp2	T	A	18: 24,615,210	V213E	probably damaging	Het
Fbxo43	A	T	15: 36,162,095		probably null	Het
Gm11559	C	A	11: 99,864,586	C20*	probably null	Het
Gnb2	T	C	5: 137,529,192	I213V	probably benign	Het
Gnb5	C	T	9: 75,344,514	T306I	probably damaging	Het
Ica1	A	T	6: 8,667,257	I303N	possibly damaging	Het
Idh1	A	G	1: 65,165,136	Y272H	probably damaging	Het
Ikzf2	G	A	1: 69,539,097	Q273*	probably null	Het
Itpkb	A	T	1: 180,327,225		probably benign	Het
Kntc1	C	T	5: 123,819,057	T2143I	probably damaging	Het
Lin9	T	A	1: 180,669,198	L351I	probably benign	Het
Lmbrd1	C	A	1: 24,748,862	D464E	possibly damaging	Het
Med13	A	G	11: 86,278,931		probably benign	Het
Mn1	T	C	5: 111,420,326	F721L	possibly damaging	Het
Myo9a	T	A	9: 59,868,184	L1026Q	possibly damaging	Het
Olfr773	A	T	10: 129,186,849	F191I	probably benign	Het
P4htm	A	C	9: 108,579,723	D428E	probably damaging	Het
Parp8	C	T	13: 116,876,580	R602H	probably damaging	Het
Pkd2	T	A	5: 104,498,506	S726R	probably damaging	Het
Pla2g6	A	T	15: 79,299,142	I495N	possibly damaging	Het
Psmd5	A	G	2: 34,856,488	I359T	probably benign	Het
Rassf6	T	C	5: 90,604,118	H292R	possibly damaging	Het
Rnf145	T	C	11: 44,560,088	I413T	probably damaging	Het
Rpn2	T	A	2: 157,283,596	V9D	possibly damaging	Het
Rpp30	T	C	19: 36,086,990	L57P	probably damaging	Het
Slc41a1	A	G	1: 131,846,587	H464R	possibly damaging	Het
Slc47a1	G	T	11: 61,369,261	P163Q	probably damaging	Het
Stra6l	T	A	4: 45,881,455	I439K	probably benign	Het
Syt9	C	T	7: 107,425,296	T132I	probably damaging	Het
Trpm2	T	C	10: 77,938,353	I471V	possibly damaging	Het
Uap1l1	A	G	2: 25,363,349	M358T	probably benign	Het
Vmn1r91	A	T	7: 20,101,945	H263L	possibly damaging	Het
Zfp407	T	C	18: 84,561,044	D648G	probably benign	Het
Zpbp2	T	C	11: 98,554,758	I150T	probably damaging	Het

Other mutations in Smc4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00401:Smc4	APN	3	69030379	missense	probably damaging	0.98
IGL00542:Smc4	APN	3	69028438	splice site	probably benign
IGL01104:Smc4	APN	3	69027584	missense	possibly damaging	0.95
IGL01380:Smc4	APN	3	69025828	missense	probably damaging	1.00
IGL01397:Smc4	APN	3	69031544	missense	probably benign
IGL02441:Smc4	APN	3	69006211	missense	probably damaging	1.00
IGL02629:Smc4	APN	3	69025873	missense	probably damaging	0.96
IGL03220:Smc4	APN	3	69009542	missense	possibly damaging	0.67
pyrrhic	UTSW	3	69027502	missense	probably damaging	1.00
R0452:Smc4	UTSW	3	69008028	nonsense	probably null
R0523:Smc4	UTSW	3	69025888	missense	probably damaging	1.00
R0568:Smc4	UTSW	3	69022461	critical splice donor site	probably null
R0571:Smc4	UTSW	3	69024289	missense	probably damaging	1.00
R0602:Smc4	UTSW	3	69009538	missense	probably damaging	1.00
R0925:Smc4	UTSW	3	69006215	critical splice donor site	probably benign
R0963:Smc4	UTSW	3	69025926	missense	probably damaging	1.00
R1540:Smc4	UTSW	3	69016772	missense	probably damaging	1.00
R1755:Smc4	UTSW	3	69034108	missense	probably damaging	1.00
R1920:Smc4	UTSW	3	69033068	missense	probably damaging	1.00
R4226:Smc4	UTSW	3	69031467	missense	probably benign	0.01
R4510:Smc4	UTSW	3	69016647	splice site	probably null
R4511:Smc4	UTSW	3	69016647	splice site	probably null
R4899:Smc4	UTSW	3	69031811	missense	probably damaging	0.97
R4967:Smc4	UTSW	3	69018239	intron	probably benign
R5096:Smc4	UTSW	3	69021279	missense	probably damaging	1.00
R5101:Smc4	UTSW	3	69028512	missense	probably benign	0.00
R5588:Smc4	UTSW	3	69025857	missense	probably benign
R5631:Smc4	UTSW	3	69030312	missense	probably benign	0.16
R6229:Smc4	UTSW	3	69030247	nonsense	probably null
R6300:Smc4	UTSW	3	69027891	missense	probably benign	0.00
R6554:Smc4	UTSW	3	69029515	missense	probably benign	0.00
R6596:Smc4	UTSW	3	69025893	missense	probably damaging	1.00
R6603:Smc4	UTSW	3	69022461	critical splice donor site	probably null
R6682:Smc4	UTSW	3	69007241	missense	probably damaging	0.98
R6727:Smc4	UTSW	3	69016772	missense	probably damaging	1.00
R6955:Smc4	UTSW	3	69024309	missense	possibly damaging	0.95
R7037:Smc4	UTSW	3	69018195	missense	possibly damaging	0.67
R7051:Smc4	UTSW	3	69027502	missense	probably damaging	1.00
R7454:Smc4	UTSW	3	69018124	missense	probably benign
R7630:Smc4	UTSW	3	69018067	critical splice acceptor site	probably benign
R7632:Smc4	UTSW	3	69018067	critical splice acceptor site	probably benign
R7633:Smc4	UTSW	3	69018067	critical splice acceptor site	probably benign
R7773:Smc4	UTSW	3	69016163	missense	probably damaging	1.00
R7857:Smc4	UTSW	3	69033219	missense	possibly damaging	0.61
R7940:Smc4	UTSW	3	69033219	missense	possibly damaging	0.61
X0063:Smc4	UTSW	3	69018103	missense	possibly damaging	0.47

Predicted Primers

PCR Primer
(F):5'- TGTATTATTGGACCAAATGGCAGTG -3'
(R):5'- GCCCATATTTATAGTGAGTGAATGCTG -3'

Sequencing Primer
(F):5'- CCAAATGGCAGTGGAAAATCC -3'
(R):5'- TGAATTAGCACTTAGGGCCC -3'

Posted On

2016-11-08