Incidental Mutation 'R4814:Smchd1'
ID 369676
Institutional Source Beutler Lab
Gene Symbol Smchd1
Ensembl Gene ENSMUSG00000024054
Gene Name SMC hinge domain containing 1
Synonyms MommeD1, 4931400A14Rik
MMRRC Submission 042432-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.838) question?
Stock # R4814 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 71651484-71782338 bp(-) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) A to G at 71718763 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

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 0.9479 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.7%
Validation Efficiency 100% (79/79)
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abi3bp T G 16: 56,471,116 (GRCm39) V587G probably benign Het
Abtb2 A G 2: 103,547,632 (GRCm39) D1002G probably benign Het
Acap2 A G 16: 30,926,944 (GRCm39) S524P probably benign Het
Acsm1 A T 7: 119,254,687 (GRCm39) I385L probably benign Het
Adra1a C G 14: 66,875,481 (GRCm39) A152G probably benign Het
Agbl4 A T 4: 111,513,565 (GRCm39) Y437F possibly damaging Het
Amt A G 9: 108,176,979 (GRCm39) T196A probably benign Het
Apobr G A 7: 126,185,859 (GRCm39) V457M probably benign Het
Birc6 A G 17: 74,956,667 (GRCm39) K3563E probably damaging Het
Cdadc1 AGACGGA AGA 14: 59,806,440 (GRCm39) probably null Het
Chrna9 T C 5: 66,134,492 (GRCm39) W448R probably damaging Het
Cyp4a31 A T 4: 115,427,466 (GRCm39) D224V probably damaging Het
Ddx10 C A 9: 53,115,405 (GRCm39) R643L possibly damaging Het
Dip2c A G 13: 9,586,896 (GRCm39) H200R probably benign Het
Dnah8 A T 17: 30,986,898 (GRCm39) R3182S probably damaging Het
Dnase1l1 C T X: 73,320,644 (GRCm39) probably null Het
Egfr T C 11: 16,819,354 (GRCm39) C295R probably damaging Het
Garem1 A T 18: 21,281,173 (GRCm39) N394K probably damaging Het
Gcat T C 15: 78,915,322 (GRCm39) probably null Het
Gckr C T 5: 31,455,644 (GRCm39) Q66* probably null Het
Gm26996 A T 6: 130,556,317 (GRCm39) noncoding transcript Het
Gm9386 C A 17: 81,246,141 (GRCm39) noncoding transcript Het
Gpr6 A T 10: 40,947,258 (GRCm39) M108K possibly damaging Het
H2-Q10 A C 17: 35,784,481 (GRCm39) probably benign Het
Hpf1 A G 8: 61,346,841 (GRCm39) D52G probably damaging Het
Jak2 A G 19: 29,279,377 (GRCm39) R989G probably damaging Het
Kat7 A G 11: 95,193,949 (GRCm39) probably benign Het
Kcnn3 G T 3: 89,570,031 (GRCm39) V615F probably damaging Het
Lgi1 G T 19: 38,289,326 (GRCm39) probably null Het
Lrrtm4 A T 6: 80,000,117 (GRCm39) T510S possibly damaging Het
Map7d1 A G 4: 126,128,114 (GRCm39) probably null Het
Mapt T C 11: 104,189,786 (GRCm39) V252A probably benign Het
Mbd4 A T 6: 115,826,260 (GRCm39) S223T possibly damaging Het
Meig1 T A 2: 3,412,959 (GRCm39) I21L probably benign Het
Mia3 A G 1: 183,113,684 (GRCm39) Y447H probably damaging Het
Mrpl46 A C 7: 78,430,343 (GRCm39) N142K probably benign Het
Myo18a C A 11: 77,750,062 (GRCm39) probably benign Het
Nup188 A G 2: 30,216,523 (GRCm39) T776A possibly damaging Het
Oas1h C A 5: 121,000,728 (GRCm39) H113N probably damaging Het
Or6c202 T A 10: 128,996,245 (GRCm39) T203S possibly damaging Het
Or7g18 A G 9: 18,787,213 (GRCm39) I197V probably benign Het
Or7g27 C T 9: 19,250,476 (GRCm39) T240M probably damaging Het
Or9i1b A T 19: 13,896,817 (GRCm39) L144F possibly damaging Het
Orc3 T A 4: 34,572,450 (GRCm39) probably benign Het
Osbpl3 T A 6: 50,329,980 (GRCm39) L65F probably damaging Het
Papola C A 12: 105,765,912 (GRCm39) P4Q probably damaging Het
Pepd A G 7: 34,645,022 (GRCm39) N151S probably damaging Het
Plekhm2 A G 4: 141,355,150 (GRCm39) L959P probably benign Het
Prpf40a A T 2: 53,080,032 (GRCm39) H82Q probably damaging Het
Robo1 C T 16: 72,768,923 (GRCm39) T496M probably benign Het
Samd9l T G 6: 3,372,863 (GRCm39) Q1466P probably damaging Het
Serpina1a T C 12: 103,821,022 (GRCm39) T342A probably benign Het
Serpina3i A G 12: 104,231,470 (GRCm39) T36A probably benign Het
Serpinb5 G T 1: 106,800,069 (GRCm39) L86F probably damaging Het
Slc35g1 A G 19: 38,391,275 (GRCm39) S186G possibly damaging Het
Slco6d1 T A 1: 98,350,899 (GRCm39) D126E probably benign Het
Smpdl3a C A 10: 57,687,337 (GRCm39) T355K probably damaging Het
Sntg2 A G 12: 30,423,267 (GRCm39) probably benign Het
Sox14 T A 9: 99,757,284 (GRCm39) M152L probably benign Het
Spats2l G T 1: 57,977,085 (GRCm39) A308S possibly damaging Het
Tcf12 T C 9: 71,777,323 (GRCm39) probably benign Het
Tcf7l2 T A 19: 55,912,504 (GRCm39) C478* probably null Het
Tekt5 A G 16: 10,200,771 (GRCm39) L250P probably damaging Het
Tmem132d T G 5: 128,061,328 (GRCm39) I425L probably benign Het
Tmem174 T A 13: 98,773,456 (GRCm39) I125F probably damaging Het
Trafd1 T G 5: 121,512,079 (GRCm39) I404L probably benign Het
Trpm5 G A 7: 142,636,373 (GRCm39) P500S possibly damaging Het
Trpm6 T A 19: 18,839,576 (GRCm39) N1616K probably benign Het
Vmn1r4 A G 6: 56,933,715 (GRCm39) D73G possibly damaging Het
Vmn2r85 T A 10: 130,254,567 (GRCm39) I706F probably benign Het
Zc3h14 C G 12: 98,719,107 (GRCm39) D157E probably damaging Het
Zfp982 A G 4: 147,597,090 (GRCm39) Q149R possibly 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
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
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'- TGGAGTAAGACCCCAACGAC -3'
(R):5'- CCCTCATAAATGGATCTATTTCTGACC -3'

Sequencing Primer
(F):5'- ACGACTTACACAGAAAATCTAGTATG -3'
(R):5'- GGATCTATTTCTGACCTTCAACAAAC -3'
Posted On 2016-02-04