Mutagenetix > Incidental Mutation

Incidental Mutation 'R2147:Smchd1'

233963

Institutional Source

Beutler Lab

Gene Symbol

Smchd1

Ensembl Gene

ENSMUSG00000024054

Gene Name

SMC hinge domain containing 1

Synonyms

MommeD1, 4931400A14Rik

MMRRC Submission

040150-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.874) question?

Stock #

R2147 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

71651484-71782338 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 71705583 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Asparagine at position 1005 (K1005N)

Ref Sequence

ENSEMBL: ENSMUSP00000121835 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000127430]

AlphaFold

Q6P5D8

Predicted Effect

possibly damaging
Transcript: ENSMUST00000127430
AA Change: K1005N

PolyPhen 2 Score 0.928 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000121835
Gene: ENSMUSG00000024054
AA Change: K1005N

Domain	Start	End	E-Value	Type
Pfam:HATPase_c_3	139	299	6.8e-16	PFAM
low complexity region	451	457	N/A	INTRINSIC
internal_repeat_1	859	1087	9.1e-5	PROSPERO
low complexity region	1185	1196	N/A	INTRINSIC
internal_repeat_1	1205	1409	9.1e-5	PROSPERO
coiled coil region	1649	1680	N/A	INTRINSIC
SMC_hinge	1721	1848	1.64e-15	SMART
low complexity region	1940	1954	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000183046

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.5%
20x: 95.7%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein which contains a hinge region domain found in members of the SMC (structural maintenance of chromosomes) protein family. [provided by RefSeq, Dec 2011]
PHENOTYPE: Females homozygous for an ENU-induced allele die at midgestation showing placental defects and hypomethylation at X-linked genes that are normally subject to X-inactivation, whereas homozygous males are viable. Females homozygous for a gene trap allele die before E13.5, whereas males remain healthy. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930523C07Rik	T	A	1: 159,903,003 (GRCm39)	M91K	probably benign	Het
Abr	T	C	11: 76,346,474 (GRCm39)	R437G	probably damaging	Het
Acaca	T	G	11: 84,167,362 (GRCm39)	D1045E	probably benign	Het
Adam23	A	T	1: 63,573,521 (GRCm39)		probably null	Het
Adam34	A	G	8: 44,105,538 (GRCm39)	Y36H	probably benign	Het
Alg11	G	A	8: 22,555,309 (GRCm39)	G108D	probably damaging	Het
Alox12e	A	T	11: 70,210,771 (GRCm39)	I316N	probably damaging	Het
Arid1a	A	T	4: 133,408,677 (GRCm39)	F1943L	unknown	Het
Armh4	T	C	14: 49,989,028 (GRCm39)	D647G	probably benign	Het
Auh	G	A	13: 52,989,532 (GRCm39)	P308L	probably benign	Het
BC035044	T	C	6: 128,867,867 (GRCm39)		probably benign	Het
Bcor	G	A	X: 11,923,862 (GRCm39)	A578V	possibly damaging	Het
C1qtnf12	A	G	4: 156,050,922 (GRCm39)	N297S	probably benign	Het
Cadps2	G	T	6: 23,838,998 (GRCm39)		probably benign	Het
Ccnf	A	T	17: 24,449,288 (GRCm39)		probably null	Het
Cdadc1	A	G	14: 59,835,202 (GRCm39)		probably null	Het
Cep57l1	A	G	10: 41,616,895 (GRCm39)	Y131H	probably damaging	Het
Cfap251	T	C	5: 123,394,254 (GRCm39)	V381A	probably benign	Het
Cfap44	A	G	16: 44,272,047 (GRCm39)	R1267G	probably benign	Het
Chd3	A	T	11: 69,239,854 (GRCm39)	L1658Q	probably benign	Het
Chl1	T	C	6: 103,692,362 (GRCm39)		probably null	Het
Chpf2	T	A	5: 24,797,033 (GRCm39)	F660I	probably damaging	Het
Cmas	T	A	6: 142,717,015 (GRCm39)	D302E	probably benign	Het
Cpne3	T	A	4: 19,536,562 (GRCm39)	M233L	probably benign	Het
Csmd3	CCTTTGCGCTT	CCTT	15: 47,604,632 (GRCm39)		probably null	Het
Dennd3	T	G	15: 73,395,336 (GRCm39)	L143R	probably damaging	Het
Dnah2	T	C	11: 69,406,587 (GRCm39)	M552V	probably benign	Het
Dock2	A	G	11: 34,179,472 (GRCm39)		probably null	Het
Ergic1	A	G	17: 26,855,024 (GRCm39)		probably null	Het
Fbxl15	A	T	19: 46,317,627 (GRCm39)	D103V	probably damaging	Het
Gm4781	C	A	10: 100,232,414 (GRCm39)		noncoding transcript	Het
Hpca	A	G	4: 129,012,278 (GRCm39)	I86T	possibly damaging	Het
Katnip	T	A	7: 125,464,492 (GRCm39)	H1286Q	probably damaging	Het
Lamb3	T	C	1: 193,010,212 (GRCm39)	V275A	probably benign	Het
Lipe	G	T	7: 25,087,946 (GRCm39)	A38E	probably benign	Het
Lrrk1	A	T	7: 65,935,159 (GRCm39)		probably null	Het
Lrsam1	T	C	2: 32,835,891 (GRCm39)	K292R	probably damaging	Het
Mbtps1	A	T	8: 120,265,598 (GRCm39)	H316Q	probably benign	Het
Mms22l	T	A	4: 24,580,063 (GRCm39)	Y525*	probably null	Het
Mrps14	T	C	1: 160,022,862 (GRCm39)	L9P	possibly damaging	Het
Mycbp2	G	A	14: 103,393,358 (GRCm39)	H3068Y	probably damaging	Het
Myo15a	A	G	11: 60,401,055 (GRCm39)	D2992G	possibly damaging	Het
N4bp2	T	A	5: 65,966,543 (GRCm39)	L1327Q	probably damaging	Het
Nradd	A	T	9: 110,451,243 (GRCm39)	F42I	probably benign	Het
Or5k8	T	A	16: 58,644,842 (GRCm39)	I77F	probably damaging	Het
Pank1	T	C	19: 34,804,754 (GRCm39)	H134R	probably benign	Het
Pcdh7	T	A	5: 58,286,458 (GRCm39)	M1178K	possibly damaging	Het
Pcnx3	A	T	19: 5,717,633 (GRCm39)	I1084N	probably damaging	Het
Pdcd11	A	G	19: 47,093,191 (GRCm39)	M490V	probably benign	Het
Phf2	T	C	13: 48,958,165 (GRCm39)	K950E	unknown	Het
Pitpnc1	C	T	11: 107,103,344 (GRCm39)	A252T	probably damaging	Het
Prickle2	A	G	6: 92,402,652 (GRCm39)	L112P	probably damaging	Het
Prpf8	A	G	11: 75,381,357 (GRCm39)	I231V	probably benign	Het
Scin	T	A	12: 40,130,984 (GRCm39)	M310L	probably benign	Het
Serpina3m	T	A	12: 104,355,483 (GRCm39)	I50N	probably benign	Het
Skint8	C	G	4: 111,794,274 (GRCm39)	N221K	probably damaging	Het
Slc22a23	C	T	13: 34,366,990 (GRCm39)	V673M	probably benign	Het
Slc24a5	A	G	2: 124,929,361 (GRCm39)	D368G	probably damaging	Het
Slc28a1	A	T	7: 80,776,015 (GRCm39)	Q237L	possibly damaging	Het
Stim2	T	C	5: 54,262,717 (GRCm39)	Y320H	probably damaging	Het
Syne3	T	A	12: 104,919,357 (GRCm39)	D512V	probably damaging	Het
Tada2a	T	C	11: 83,970,455 (GRCm39)	D432G	probably damaging	Het
Tcp10a	T	C	17: 7,601,701 (GRCm39)	S216P	probably damaging	Het
Tmem178b	A	T	6: 40,184,435 (GRCm39)	Q111L	probably damaging	Het
Tmem236	A	G	2: 14,223,861 (GRCm39)	I217V	probably benign	Het
Tmem45b	A	G	9: 31,340,277 (GRCm39)	V128A	probably benign	Het
Tnfaip2	T	C	12: 111,412,456 (GRCm39)	Y286H	probably damaging	Het
Tsc2	T	A	17: 24,840,116 (GRCm39)	I427L	possibly damaging	Het
Ttc17	T	A	2: 94,132,139 (GRCm39)	N1180I	possibly damaging	Het
Ubr1	T	G	2: 120,694,811 (GRCm39)	D1707A	probably damaging	Het
Vmn1r11	A	G	6: 57,114,583 (GRCm39)	I82M	probably benign	Het
Vmn2r129	T	C	4: 156,687,014 (GRCm39)		noncoding transcript	Het
Vps41	G	T	13: 19,023,904 (GRCm39)		probably null	Het
Wnt5a	A	G	14: 28,235,274 (GRCm39)	Y86C	probably damaging	Het
Zfp629	T	C	7: 127,209,616 (GRCm39)	H731R	probably damaging	Het
Zfp712	T	C	13: 67,189,960 (GRCm39)	E189G	possibly damaging	Het

Other mutations in Smchd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00162:Smchd1	APN	17	71,772,668 (GRCm39)	splice site	probably benign
IGL00529:Smchd1	APN	17	71,701,794 (GRCm39)	missense	probably benign	0.30
IGL00642:Smchd1	APN	17	71,697,427 (GRCm39)	missense	probably damaging	1.00
IGL00821:Smchd1	APN	17	71,705,618 (GRCm39)	missense	possibly damaging	0.92
IGL01330:Smchd1	APN	17	71,743,783 (GRCm39)	missense	probably benign
IGL01432:Smchd1	APN	17	71,738,285 (GRCm39)	missense	probably damaging	1.00
IGL01473:Smchd1	APN	17	71,696,745 (GRCm39)	missense	probably benign	0.00
IGL01705:Smchd1	APN	17	71,688,393 (GRCm39)	missense	probably damaging	1.00
IGL01787:Smchd1	APN	17	71,698,413 (GRCm39)	missense	probably damaging	0.99
IGL01814:Smchd1	APN	17	71,685,182 (GRCm39)	missense	probably benign	0.01
IGL01976:Smchd1	APN	17	71,701,720 (GRCm39)	nonsense	probably null
IGL01995:Smchd1	APN	17	71,751,015 (GRCm39)	missense	probably damaging	0.98
IGL02090:Smchd1	APN	17	71,738,248 (GRCm39)	missense	possibly damaging	0.86
IGL02302:Smchd1	APN	17	71,665,128 (GRCm39)	splice site	probably benign
IGL02309:Smchd1	APN	17	71,750,898 (GRCm39)	missense	probably benign	0.32
IGL02391:Smchd1	APN	17	71,738,254 (GRCm39)	missense	probably null	1.00
IGL02515:Smchd1	APN	17	71,747,952 (GRCm39)	missense	probably damaging	1.00
IGL02644:Smchd1	APN	17	71,667,016 (GRCm39)	splice site	probably benign
IGL03081:Smchd1	APN	17	71,667,186 (GRCm39)	missense	probably damaging	0.98
IGL03212:Smchd1	APN	17	71,750,886 (GRCm39)	missense	probably damaging	0.99
IGL03236:Smchd1	APN	17	71,698,425 (GRCm39)	missense	possibly damaging	0.88
IGL03297:Smchd1	APN	17	71,656,695 (GRCm39)	missense	probably benign	0.01
Dry_tortugas	UTSW	17	71,747,951 (GRCm39)	missense	probably damaging	1.00
R0049:Smchd1	UTSW	17	71,738,231 (GRCm39)	missense	probably benign	0.01
R0254:Smchd1	UTSW	17	71,718,886 (GRCm39)	missense	probably benign	0.00
R0391:Smchd1	UTSW	17	71,710,149 (GRCm39)	missense	probably damaging	1.00
R0403:Smchd1	UTSW	17	71,701,897 (GRCm39)	missense	probably damaging	1.00
R0499:Smchd1	UTSW	17	71,694,083 (GRCm39)	missense	probably benign
R0520:Smchd1	UTSW	17	71,736,538 (GRCm39)	missense	possibly damaging	0.85
R0616:Smchd1	UTSW	17	71,686,569 (GRCm39)	missense	probably benign	0.39
R1120:Smchd1	UTSW	17	71,665,141 (GRCm39)	nonsense	probably null
R1469:Smchd1	UTSW	17	71,656,725 (GRCm39)	missense	probably damaging	1.00
R1469:Smchd1	UTSW	17	71,656,725 (GRCm39)	missense	probably damaging	1.00
R1473:Smchd1	UTSW	17	71,668,832 (GRCm39)	splice site	probably benign
R1484:Smchd1	UTSW	17	71,685,252 (GRCm39)	missense	probably benign	0.31
R1501:Smchd1	UTSW	17	71,672,089 (GRCm39)	missense	possibly damaging	0.54
R1718:Smchd1	UTSW	17	71,755,828 (GRCm39)	missense	possibly damaging	0.46
R1765:Smchd1	UTSW	17	71,707,196 (GRCm39)	splice site	probably benign
R1766:Smchd1	UTSW	17	71,698,374 (GRCm39)	missense	probably damaging	0.99
R1803:Smchd1	UTSW	17	71,694,001 (GRCm39)	missense	probably damaging	0.99
R1829:Smchd1	UTSW	17	71,677,332 (GRCm39)	missense	probably damaging	1.00
R1850:Smchd1	UTSW	17	71,696,766 (GRCm39)	missense	probably damaging	0.99
R1917:Smchd1	UTSW	17	71,714,232 (GRCm39)	missense	possibly damaging	0.48
R1918:Smchd1	UTSW	17	71,714,232 (GRCm39)	missense	possibly damaging	0.48
R1936:Smchd1	UTSW	17	71,770,786 (GRCm39)	missense	probably damaging	1.00
R2024:Smchd1	UTSW	17	71,677,923 (GRCm39)	missense	probably benign	0.15
R2180:Smchd1	UTSW	17	71,770,794 (GRCm39)	missense	probably benign	0.23
R2398:Smchd1	UTSW	17	71,733,431 (GRCm39)	splice site	probably benign
R2398:Smchd1	UTSW	17	71,667,136 (GRCm39)	missense	probably damaging	1.00
R2935:Smchd1	UTSW	17	71,718,900 (GRCm39)	missense	probably damaging	1.00
R3000:Smchd1	UTSW	17	71,670,033 (GRCm39)	missense	probably benign	0.00
R3021:Smchd1	UTSW	17	71,694,093 (GRCm39)	missense	possibly damaging	0.75
R3808:Smchd1	UTSW	17	71,736,536 (GRCm39)	missense	probably damaging	1.00
R4323:Smchd1	UTSW	17	71,735,270 (GRCm39)	missense	probably benign	0.00
R4486:Smchd1	UTSW	17	71,714,230 (GRCm39)	missense	probably benign	0.02
R4487:Smchd1	UTSW	17	71,714,230 (GRCm39)	missense	probably benign	0.02
R4488:Smchd1	UTSW	17	71,714,230 (GRCm39)	missense	probably benign	0.02
R4489:Smchd1	UTSW	17	71,714,230 (GRCm39)	missense	probably benign	0.02
R4723:Smchd1	UTSW	17	71,743,742 (GRCm39)	nonsense	probably null
R4751:Smchd1	UTSW	17	71,698,463 (GRCm39)	missense	probably benign	0.01
R4798:Smchd1	UTSW	17	71,667,048 (GRCm39)	nonsense	probably null
R4814:Smchd1	UTSW	17	71,718,763 (GRCm39)	critical splice donor site	probably null
R4882:Smchd1	UTSW	17	71,665,234 (GRCm39)	intron	probably benign
R5088:Smchd1	UTSW	17	71,738,343 (GRCm39)	missense	possibly damaging	0.86
R5589:Smchd1	UTSW	17	71,747,956 (GRCm39)	missense	probably damaging	1.00
R5618:Smchd1	UTSW	17	71,762,722 (GRCm39)	missense	probably damaging	1.00
R5839:Smchd1	UTSW	17	71,701,857 (GRCm39)	missense	probably damaging	0.98
R5994:Smchd1	UTSW	17	71,672,404 (GRCm39)	missense	possibly damaging	0.89
R6009:Smchd1	UTSW	17	71,747,951 (GRCm39)	missense	probably damaging	1.00
R6042:Smchd1	UTSW	17	71,684,052 (GRCm39)	nonsense	probably null
R6082:Smchd1	UTSW	17	71,656,714 (GRCm39)	missense	probably benign	0.09
R6126:Smchd1	UTSW	17	71,677,280 (GRCm39)	missense	probably damaging	1.00
R6294:Smchd1	UTSW	17	71,677,922 (GRCm39)	missense	probably benign	0.13
R6788:Smchd1	UTSW	17	71,782,096 (GRCm39)	missense	probably benign	0.02
R6853:Smchd1	UTSW	17	71,743,738 (GRCm39)	missense	probably damaging	1.00
R6875:Smchd1	UTSW	17	71,660,501 (GRCm39)	missense	probably damaging	1.00
R7026:Smchd1	UTSW	17	71,656,662 (GRCm39)	missense	probably benign
R7045:Smchd1	UTSW	17	71,722,039 (GRCm39)	missense	probably benign	0.22
R7068:Smchd1	UTSW	17	71,694,087 (GRCm39)	missense	probably benign	0.00
R7085:Smchd1	UTSW	17	71,672,214 (GRCm39)	splice site	probably null
R7089:Smchd1	UTSW	17	71,668,955 (GRCm39)	missense	probably benign	0.00
R7145:Smchd1	UTSW	17	71,685,202 (GRCm39)	missense	probably benign
R7158:Smchd1	UTSW	17	71,707,145 (GRCm39)	missense	probably damaging	0.99
R7180:Smchd1	UTSW	17	71,701,818 (GRCm39)	missense	probably damaging	0.99
R7183:Smchd1	UTSW	17	71,660,511 (GRCm39)	missense	probably benign	0.00
R7214:Smchd1	UTSW	17	71,652,359 (GRCm39)	missense	probably benign	0.15
R7414:Smchd1	UTSW	17	71,782,074 (GRCm39)	missense	probably damaging	0.99
R7512:Smchd1	UTSW	17	71,688,364 (GRCm39)	missense	possibly damaging	0.51
R7631:Smchd1	UTSW	17	71,705,684 (GRCm39)	missense	probably benign	0.10
R7641:Smchd1	UTSW	17	71,697,474 (GRCm39)	missense	probably benign	0.00
R7709:Smchd1	UTSW	17	71,665,193 (GRCm39)	missense	probably damaging	1.00
R7768:Smchd1	UTSW	17	71,718,906 (GRCm39)	missense	probably damaging	1.00
R7789:Smchd1	UTSW	17	71,782,296 (GRCm39)	start gained	probably benign
R7898:Smchd1	UTSW	17	71,684,813 (GRCm39)	splice site	probably null
R7965:Smchd1	UTSW	17	71,762,621 (GRCm39)	missense	possibly damaging	0.65
R8177:Smchd1	UTSW	17	71,697,448 (GRCm39)	missense	probably benign	0.28
R8359:Smchd1	UTSW	17	71,738,238 (GRCm39)	missense	probably damaging	0.99
R8370:Smchd1	UTSW	17	71,701,908 (GRCm39)	missense	probably benign	0.22
R8426:Smchd1	UTSW	17	71,755,598 (GRCm39)	missense	probably damaging	1.00
R8443:Smchd1	UTSW	17	71,714,244 (GRCm39)	missense	probably benign	0.18
R8948:Smchd1	UTSW	17	71,743,767 (GRCm39)	missense	probably damaging	1.00
R8954:Smchd1	UTSW	17	71,755,752 (GRCm39)	missense	probably damaging	1.00
R9041:Smchd1	UTSW	17	71,701,710 (GRCm39)	critical splice donor site	probably null
R9054:Smchd1	UTSW	17	71,670,017 (GRCm39)	nonsense	probably null
R9141:Smchd1	UTSW	17	71,672,125 (GRCm39)	missense	probably benign	0.00
R9169:Smchd1	UTSW	17	71,722,659 (GRCm39)	missense	probably damaging	1.00
R9231:Smchd1	UTSW	17	71,672,084 (GRCm39)	missense	probably benign	0.05
R9368:Smchd1	UTSW	17	71,694,071 (GRCm39)	missense	probably damaging	1.00
R9374:Smchd1	UTSW	17	71,718,843 (GRCm39)	missense	possibly damaging	0.61
R9416:Smchd1	UTSW	17	71,701,791 (GRCm39)	missense	probably benign	0.27
R9426:Smchd1	UTSW	17	71,672,125 (GRCm39)	missense	probably benign	0.00
R9491:Smchd1	UTSW	17	71,667,020 (GRCm39)	critical splice donor site	probably null
R9511:Smchd1	UTSW	17	71,750,899 (GRCm39)	missense	possibly damaging	0.65
R9591:Smchd1	UTSW	17	71,701,828 (GRCm39)	missense	probably damaging	1.00
R9593:Smchd1	UTSW	17	71,701,828 (GRCm39)	missense	probably damaging	1.00
Z1176:Smchd1	UTSW	17	71,668,836 (GRCm39)	missense	probably null	1.00

Predicted Primers

PCR Primer
(F):5'- AGCTTCAAGGGACCCAATGTC -3'
(R):5'- AGGCAGCAGTGTTAGCTGTG -3'

Sequencing Primer
(F):5'- GGACCCAATGTCTCTGTTCTCAC -3'
(R):5'- GCAGTGTTAGCTGTGGTAAATTATTC -3'

Posted On

2014-10-01