Incidental Mutation 'R1917:Smchd1'
ID 212656
Institutional Source Beutler Lab
Gene Symbol Smchd1
Ensembl Gene ENSMUSG00000024054
Gene Name SMC hinge domain containing 1
Synonyms MommeD1, 4931400A14Rik
MMRRC Submission 039935-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.838) question?
Stock # R1917 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 71651484-71782338 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 71714232 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 877 (I877T)
Ref Sequence ENSEMBL: ENSMUSP00000121835 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000127430]
AlphaFold Q6P5D8
Predicted Effect possibly damaging
Transcript: ENSMUST00000127430
AA Change: I877T

PolyPhen 2 Score 0.480 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000121835
Gene: ENSMUSG00000024054
AA Change: I877T

DomainStartEndE-ValueType
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 0.0619 question?
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 97.0%
  • 10x: 95.8%
  • 20x: 93.6%
Validation Efficiency 100% (83/83)
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: 81 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca8a A G 11: 109,982,341 (GRCm39) probably benign Het
Adgre5 A G 8: 84,455,738 (GRCm39) V190A probably damaging Het
Akap6 A G 12: 53,151,395 (GRCm39) N1153S probably benign Het
Aldh1a7 G A 19: 20,704,819 (GRCm39) H20Y probably benign Het
B430306N03Rik A G 17: 48,631,176 (GRCm39) E278G probably benign Het
Cacna1b C A 2: 24,506,891 (GRCm39) R72L probably null Het
Cc2d2a C G 5: 43,863,564 (GRCm39) S675R probably damaging Het
Ccdc88b T A 19: 6,826,594 (GRCm39) E1040D probably damaging Het
Cmtm7 A G 9: 114,592,432 (GRCm39) V55A probably damaging Het
Coq4 A C 2: 29,679,938 (GRCm39) T77P probably damaging Het
Cyp2j11 C A 4: 96,228,211 (GRCm39) W136L probably damaging Het
Dctn2 T A 10: 127,110,918 (GRCm39) Y86* probably null Het
Ddx56 A G 11: 6,213,937 (GRCm39) probably null Het
Dop1b T C 16: 93,513,150 (GRCm39) S30P probably damaging Het
Ep400 T C 5: 110,851,441 (GRCm39) K1347R unknown Het
Fat3 T A 9: 15,908,353 (GRCm39) T2550S possibly damaging Het
Fcrla G T 1: 170,755,095 (GRCm39) C5* probably null Het
Fem1al A G 11: 29,774,039 (GRCm39) S473P probably benign Het
Fermt1 T A 2: 132,764,762 (GRCm39) D365V probably damaging Het
Fhod3 A G 18: 25,123,022 (GRCm39) probably benign Het
Fhod3 A G 18: 25,218,658 (GRCm39) D807G probably benign Het
Fnip1 C T 11: 54,371,510 (GRCm39) T177I probably damaging Het
Gart T C 16: 91,425,037 (GRCm39) Y662C probably damaging Het
Gda A T 19: 21,375,004 (GRCm39) probably benign Het
Gk A G X: 84,804,186 (GRCm39) I85T probably damaging Het
Gm3476 A G 14: 6,118,358 (GRCm38) L255P possibly damaging Het
Gm9966 T C 7: 95,607,684 (GRCm39) C2R unknown Het
Gnpda1 T C 18: 38,466,243 (GRCm39) probably null Het
Gtf2h4 G A 17: 35,981,090 (GRCm39) L246F possibly damaging Het
Hao1 A T 2: 134,364,980 (GRCm39) S216T probably benign Het
Hnrnpr C A 4: 136,059,799 (GRCm39) S301* probably null Het
Hsd3b2 A G 3: 98,619,342 (GRCm39) I201T probably benign Het
Jade2 T C 11: 51,709,365 (GRCm39) E548G possibly damaging Het
Katnbl1 T C 2: 112,239,524 (GRCm39) I241T probably benign Het
Keap1 G T 9: 21,145,102 (GRCm39) Q299K probably benign Het
Kif1a T C 1: 92,946,753 (GRCm39) I1650V possibly damaging Het
Lrba G A 3: 86,571,808 (GRCm39) G275R probably damaging Het
Map3k9 C A 12: 81,827,564 (GRCm39) E29* probably null Het
Mat1a G A 14: 40,843,394 (GRCm39) V307I probably damaging Het
Mcm2 A T 6: 88,868,785 (GRCm39) M324K possibly damaging Het
Metap1d T C 2: 71,341,871 (GRCm39) V155A probably damaging Het
Mtbp A G 15: 55,428,073 (GRCm39) probably benign Het
Myh14 T C 7: 44,307,349 (GRCm39) T231A probably benign Het
Mylk4 A T 13: 32,908,836 (GRCm39) D90E probably benign Het
Myo15b T A 11: 115,773,080 (GRCm39) I1837K possibly damaging Het
Myo3a T A 2: 22,296,733 (GRCm39) H242Q probably damaging Het
Nxn A G 11: 76,152,498 (GRCm39) probably benign Het
Or6c2 T A 10: 129,362,918 (GRCm39) V274D probably damaging Het
Pak3 C A X: 142,574,298 (GRCm39) A553E possibly damaging Het
Pdia2 T A 17: 26,417,079 (GRCm39) T122S possibly damaging Het
Pira12 C T 7: 3,900,637 (GRCm39) V38M probably damaging Het
Plod2 A G 9: 92,463,310 (GRCm39) T132A probably benign Het
Ptprz1 T A 6: 23,035,039 (GRCm39) probably benign Het
Rad54b A C 4: 11,601,693 (GRCm39) N416T probably damaging Het
Recql4 A T 15: 76,588,037 (GRCm39) Y1142* probably null Het
Rnf216 A G 5: 142,978,561 (GRCm39) V859A probably benign Het
Scnm1 G T 3: 95,037,584 (GRCm39) P161T possibly damaging Het
Serpinb6b A G 13: 33,162,223 (GRCm39) I222V probably benign Het
Serpinf1 A G 11: 75,301,833 (GRCm39) I274T possibly damaging Het
Slc28a1 T C 7: 80,819,334 (GRCm39) F641L probably benign Het
Slc8a2 A G 7: 15,886,845 (GRCm39) I657V probably benign Het
Spata31 T C 13: 65,068,679 (GRCm39) Y276H possibly damaging Het
Spire2 A G 8: 124,089,810 (GRCm39) D447G probably benign Het
Stk3 G A 15: 35,073,363 (GRCm39) T119I probably damaging Het
Stxbp5 C A 10: 9,688,042 (GRCm39) V420F possibly damaging Het
Sult2a5 T C 7: 13,404,609 (GRCm39) F282S probably damaging Het
Syk A T 13: 52,776,744 (GRCm39) D248V probably damaging Het
Thoc6 C T 17: 23,888,364 (GRCm39) probably benign Het
Timd5 A G 11: 46,419,358 (GRCm39) D58G possibly damaging Het
Tll2 T A 19: 41,116,936 (GRCm39) D293V possibly damaging Het
Umodl1 G A 17: 31,203,017 (GRCm39) V457M probably damaging Het
Usp19 T A 9: 108,376,524 (GRCm39) C689* probably null Het
Usp24 T G 4: 106,267,483 (GRCm39) V1955G probably damaging Het
Vmn1r226 T C 17: 20,907,842 (GRCm39) S25P probably damaging Het
Vmn2r69 C T 7: 85,060,891 (GRCm39) C231Y probably damaging Het
Wdr73 C T 7: 80,543,081 (GRCm39) D176N probably benign Het
Wnt7b T A 15: 85,443,281 (GRCm39) I41F probably damaging Het
Zfhx3 T C 8: 109,682,880 (GRCm39) S3440P unknown Het
Zfp52 T G 17: 21,780,426 (GRCm39) N91K probably benign Het
Zfp930 C A 8: 69,681,357 (GRCm39) Q350K probably benign Het
Zfp949 T C 9: 88,452,115 (GRCm39) S562P probably damaging Het
Other mutations in Smchd1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- CTGAGTCAGATAACACAGCACTG -3'
(R):5'- ACTTACAATGTTTGCTTGGCC -3'

Sequencing Primer
(F):5'- GCACTGACAAATTTCCAACATCTTAG -3'
(R):5'- GCTATATAAGGGGATCTCTGACTC -3'
Posted On 2014-07-14