Mutagenetix > Incidental Mutation

Incidental Mutation 'R7898:Smchd1'

628772

Institutional Source

Beutler Lab

Gene Symbol

Smchd1

Ensembl Gene

ENSMUSG00000024054

Gene Name

SMC hinge domain containing 1

Synonyms

MommeD1, 4931400A14Rik

MMRRC Submission

045950-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.838) question?

Stock #

R7898 (G1)

Quality Score

59.01

Status

Validated

Chromosome

Chromosomal Location

71651484-71782338 bp(-) (GRCm39)

Type of Mutation

splice site (330 bp from exon)

DNA Base Change (assembly)

T to C at 71684813 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000121835 (fasta)

Gene Model

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

AlphaFold

Q6P5D8

Predicted Effect

probably null
Transcript: ENSMUST00000127430

SMART Domains

Protein: ENSMUSP00000121835
Gene: ENSMUSG00000024054

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

Coding Region Coverage

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

Validation Efficiency

99% (69/70)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acaca	T	C	11: 84,255,275 (GRCm39)		probably null	Het
Afg2a	T	G	3: 37,474,620 (GRCm39)	M44R	probably benign	Het
Ankef1	C	A	2: 136,395,618 (GRCm39)	N649K	probably benign	Het
Arl5b	T	A	2: 15,079,869 (GRCm39)	S147T	probably damaging	Het
Arnt2	A	T	7: 83,918,155 (GRCm39)		probably null	Het
Ash1l	A	G	3: 88,890,932 (GRCm39)	E937G	possibly damaging	Het
Asxl1	T	G	2: 153,241,854 (GRCm39)	S802R	possibly damaging	Het
Cacna1h	T	A	17: 25,611,250 (GRCm39)	H516L	probably damaging	Het
Cad	A	G	5: 31,218,829 (GRCm39)	Y550C	probably damaging	Het
Cdo1	A	G	18: 46,861,157 (GRCm39)	I18T	probably benign	Het
Cfap251	A	T	5: 123,460,517 (GRCm39)	I1160F	probably damaging	Het
Chd2	A	G	7: 73,169,223 (GRCm39)		probably null	Het
Dbf4	A	G	5: 8,458,232 (GRCm39)		probably null	Het
Dcdc2a	A	T	13: 25,286,361 (GRCm39)	R132W	possibly damaging	Het
Dnah10	T	C	5: 124,859,425 (GRCm39)	S2131P	probably damaging	Het
Eef2k	A	G	7: 120,494,441 (GRCm39)	Y599C	probably damaging	Het
Eno2	C	T	6: 124,744,225 (GRCm39)		probably null	Het
Fam124b	T	A	1: 80,191,512 (GRCm39)		probably benign	Het
Fezf2	A	G	14: 12,342,701 (GRCm38)	I388T	possibly damaging	Het
Gbp11	T	C	5: 105,472,798 (GRCm39)	N542S	probably benign	Het
Gdpd1	T	A	11: 86,932,639 (GRCm39)	I229F	probably damaging	Het
Gria1	T	A	11: 57,133,591 (GRCm39)	V490E	probably damaging	Het
Grm8	G	A	6: 27,762,422 (GRCm39)	R268C	probably damaging	Het
Hectd4	T	A	5: 121,469,880 (GRCm39)	S2592T	probably benign	Het
Herpud1	C	T	8: 95,118,828 (GRCm39)	T194I	probably benign	Het
Hspa1b	T	C	17: 35,177,167 (GRCm39)	T273A	probably benign	Het
Iftap	T	A	2: 101,416,747 (GRCm39)	K67N	probably benign	Het
Ighm	T	A	12: 113,384,873 (GRCm39)	K327*	probably null	Het
Igkv3-4	A	T	6: 70,649,297 (GRCm39)	I99F	probably damaging	Het
Iqca1l	T	C	5: 24,758,643 (GRCm39)	E117G	probably damaging	Het
Isl2	C	A	9: 55,449,723 (GRCm39)	S97R	probably benign	Het
Klhl12	A	T	1: 134,386,219 (GRCm39)	I4F	probably benign	Het
Lgalsl2	G	A	7: 5,362,441 (GRCm39)	R24H	probably benign	Het
Lrp2	T	C	2: 69,271,710 (GRCm39)	E4074G	probably benign	Het
Mcm3ap	A	G	10: 76,342,441 (GRCm39)	N1645D	probably damaging	Het
Mettl23	T	C	11: 116,736,679 (GRCm39)		probably benign	Het
Mettl24	A	G	10: 40,686,478 (GRCm39)	E285G	probably benign	Het
Mis18bp1	A	G	12: 65,196,246 (GRCm39)	L506P	probably benign	Het
Mup18	G	T	4: 61,590,925 (GRCm39)		probably null	Het
Myom1	T	C	17: 71,352,747 (GRCm39)	L357P	probably benign	Het
Nkx2-9	G	A	12: 56,659,031 (GRCm39)	A61V	probably benign	Het
Or52n5	C	T	7: 104,588,573 (GRCm39)	A280V	probably damaging	Het
Pbx1	A	T	1: 168,012,616 (GRCm39)	M340K	probably benign	Het
Pcdhb17	A	T	18: 37,618,233 (GRCm39)	N8Y	probably benign	Het
Pex13	C	A	11: 23,600,929 (GRCm39)		probably null	Het
Pierce1	TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC	TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC	2: 28,356,122 (GRCm39)		probably benign	Het
Plxnb1	A	G	9: 108,943,408 (GRCm39)	R1884G	probably damaging	Het
Polq	T	A	16: 36,865,245 (GRCm39)	V699E	probably damaging	Het
Ppl	C	T	16: 4,906,725 (GRCm39)	R1190H	probably damaging	Het
Prr14l	A	T	5: 32,987,310 (GRCm39)	H728Q	probably benign	Het
Prss12	T	C	3: 123,300,145 (GRCm39)	V752A	possibly damaging	Het
Prss56	A	G	1: 87,111,921 (GRCm39)	S51G	probably benign	Het
Pwp2	G	A	10: 78,009,240 (GRCm39)	R854W	probably damaging	Het
Rhobtb2	C	T	14: 70,033,746 (GRCm39)	C493Y	probably damaging	Het
Rictor	C	T	15: 6,801,635 (GRCm39)	S441L	probably benign	Het
Rusf1	C	A	7: 127,897,177 (GRCm39)	A27S	probably benign	Het
Scap	A	G	9: 110,213,811 (GRCm39)	N1258S	possibly damaging	Het
Sec31a	C	T	5: 100,547,336 (GRCm39)	G218R	probably damaging	Het
Siglec15	A	T	18: 78,086,914 (GRCm39)	M315K	probably benign	Het
Slc17a6	G	A	7: 51,308,573 (GRCm39)		probably null	Het
Spag4	A	T	2: 155,911,244 (GRCm39)	D393V	probably damaging	Het
Sulf1	A	G	1: 12,875,518 (GRCm39)	N176S	probably damaging	Het
Tmem9	T	A	1: 135,955,125 (GRCm39)		probably null	Het
Tnpo3	T	C	6: 29,565,223 (GRCm39)	I577V	probably benign	Het
Tti1	A	C	2: 157,835,390 (GRCm39)	I956S	probably benign	Het
Wdr81	T	C	11: 75,344,725 (GRCm39)	R181G	probably benign	Het
Zfp462	T	A	4: 55,012,995 (GRCm39)	C1654S	probably damaging	Het
Zfp74	A	T	7: 29,635,380 (GRCm39)	C109*	probably null	Het
Znrf4	A	G	17: 56,818,681 (GRCm39)	C209R	probably damaging	Het
Zzef1	T	G	11: 72,687,373 (GRCm39)	L84R	probably 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
R2147:Smchd1	UTSW	17	71,705,583 (GRCm39)	missense	possibly damaging	0.93
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
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'- GGAACCAATGGCTGCAAGTG -3'
(R):5'- AGGGAAACATAGAGACTCTTGTTTC -3'

Sequencing Primer
(F):5'- TCAGGCTGGAAACATGTCTC -3'
(R):5'- AGAGACTCTTGTTTCAAAACCAC -3'

Posted On

2020-06-22