Mutagenetix > Incidental Mutation

Incidental Mutation 'R7641:Smchd1'

590270

Institutional Source

Beutler Lab

Gene Symbol

Smchd1

Ensembl Gene

ENSMUSG00000024054

Gene Name

SMC hinge domain containing 1

Synonyms

MommeD1, 4931400A14Rik

MMRRC Submission

045699-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.838) question?

Stock #

R7641 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

71651484-71782338 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 71697474 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Aspartic acid at position 1155 (E1155D)

Ref Sequence

ENSEMBL: ENSMUSP00000121835 (fasta)

Gene Model

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

AlphaFold

Q6P5D8

Predicted Effect

probably benign
Transcript: ENSMUST00000127430
AA Change: E1155D

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000121835
Gene: ENSMUSG00000024054
AA Change: E1155D

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

Meta Mutation Damage Score

0.0880

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (52/52)

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: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam1a	T	A	5: 121,657,370 (GRCm39)	Q641L	probably benign	Het
Aknad1	A	T	3: 108,679,291 (GRCm39)	H474L	probably benign	Het
Alkal1	A	T	1: 6,459,712 (GRCm39)	Y96F	probably damaging	Het
Cars1	A	G	7: 143,140,840 (GRCm39)		probably null	Het
Chtf18	A	T	17: 25,941,249 (GRCm39)		probably null	Het
Cog2	C	A	8: 125,264,621 (GRCm39)	N333K	probably damaging	Het
Col6a5	T	A	9: 105,758,625 (GRCm39)	R2194*	probably null	Het
Dnah14	A	T	1: 181,535,098 (GRCm39)	I2355L	probably benign	Het
Dock8	G	A	19: 25,151,697 (GRCm39)		probably null	Het
Dpy19l3	A	C	7: 35,394,734 (GRCm39)	D601E	probably damaging	Het
Elf1	G	A	14: 79,808,163 (GRCm39)	G205E	probably damaging	Het
Fsip2	A	T	2: 82,817,256 (GRCm39)	K4330*	probably null	Het
Gm6525	A	T	3: 84,082,150 (GRCm39)	T24S	probably benign	Het
Golga4	G	T	9: 118,386,643 (GRCm39)	R1255L	probably benign	Het
Gpn2	A	T	4: 133,315,970 (GRCm39)	Q243L	probably null	Het
Grb10	T	C	11: 11,883,492 (GRCm39)	K588E	possibly damaging	Het
Gys1	T	C	7: 45,104,495 (GRCm39)	S641P	probably damaging	Het
H2-M5	T	A	17: 37,298,323 (GRCm39)	M331L	probably benign	Het
Ighv6-6	T	A	12: 114,398,837 (GRCm39)	I10L	probably benign	Het
Jmy	C	T	13: 93,579,107 (GRCm39)	R675Q	probably damaging	Het
Lonp2	A	T	8: 87,392,386 (GRCm39)	Q484L	probably benign	Het
Map3k20	T	A	2: 72,228,705 (GRCm39)	L308H	probably damaging	Het
Mep1b	T	C	18: 21,228,034 (GRCm39)	F546L	possibly damaging	Het
Mier1	A	G	4: 102,996,637 (GRCm39)	E133G	possibly damaging	Het
Msh3	C	A	13: 92,349,011 (GRCm39)	V1074L	probably benign	Het
Muc6	A	T	7: 141,224,247 (GRCm39)	L1645Q	unknown	Het
Nat10	G	A	2: 103,573,435 (GRCm39)	A354V	probably damaging	Het
Or8b12i	A	G	9: 20,082,549 (GRCm39)	L106P	possibly damaging	Het
Pdyn	A	T	2: 129,531,748 (GRCm39)	V14E	possibly damaging	Het
Prdm16	T	A	4: 154,429,901 (GRCm39)	H356L	probably damaging	Het
Rasa3	A	G	8: 13,634,961 (GRCm39)	C453R	probably benign	Het
Rasgrf2	C	T	13: 92,267,914 (GRCm39)	S30N	possibly damaging	Het
Rlf	A	G	4: 121,016,393 (GRCm39)	S315P	probably damaging	Het
Rusc2	C	T	4: 43,425,335 (GRCm39)	R1147W	possibly damaging	Het
Sacs	T	A	14: 61,440,320 (GRCm39)	Y789N	probably damaging	Het
Sap130	T	C	18: 31,786,676 (GRCm39)	L289P	probably damaging	Het
Septin3	A	G	15: 82,174,983 (GRCm39)	Y308C	probably damaging	Het
Slc2a12	A	G	10: 22,569,893 (GRCm39)	D528G	probably damaging	Het
Slc2a13	A	G	15: 91,156,359 (GRCm39)	*638Q	probably null	Het
Sorcs2	G	A	5: 36,555,296 (GRCm39)	R32C	probably damaging	Het
Sp110	G	A	1: 85,506,813 (GRCm39)	R417C	probably benign	Het
Tonsl	C	T	15: 76,517,852 (GRCm39)	D650N	probably damaging	Het
Tti1	A	T	2: 157,850,949 (GRCm39)	F97I	possibly damaging	Het
Ttn	T	C	2: 76,572,554 (GRCm39)	Q26113R	possibly damaging	Het
Unc5d	A	T	8: 29,210,003 (GRCm39)	N444K	probably damaging	Het
Usp17la	A	T	7: 104,510,654 (GRCm39)	K420*	probably null	Het
Vmn2r114	T	C	17: 23,527,177 (GRCm39)	N452D	possibly damaging	Het
Vps16	T	C	2: 130,282,448 (GRCm39)	V427A	probably benign	Het
Wdr5b	T	A	16: 35,862,712 (GRCm39)	V277D	probably damaging	Het
Zan	T	A	5: 137,465,370 (GRCm39)	M462L	possibly damaging	Het
Zfp40	A	G	17: 23,397,257 (GRCm39)	V80A	possibly damaging	Het
Zfp930	A	T	8: 69,681,337 (GRCm39)	H344L	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
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'- GCCTAAAGGAAACGCTTAATGG -3'
(R):5'- CTTGCATCAGTAGCAATGAGAAGTG -3'

Sequencing Primer
(F):5'- ACGCTTAATGGTATGTATTTTCTAGC -3'
(R):5'- AGTGAAAGATTTGGAGGGCTCTG -3'

Posted On

2019-10-24