Incidental Mutation 'R1109:Smc1b'
ID 98689
Institutional Source Beutler Lab
Gene Symbol Smc1b
Ensembl Gene ENSMUSG00000022432
Gene Name structural maintenance of chromosomes 1B
Synonyms Smc1l2, SMC1beta
MMRRC Submission 039182-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.696) question?
Stock # R1109 (G1)
Quality Score 225
Status Validated
Chromosome 15
Chromosomal Location 84948890-85016158 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 84997016 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 535 (T535A)
Ref Sequence ENSEMBL: ENSMUSP00000023068 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023068]
AlphaFold Q920F6
Predicted Effect probably damaging
Transcript: ENSMUST00000023068
AA Change: T535A

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000023068
Gene: ENSMUSG00000022432
AA Change: T535A

DomainStartEndE-ValueType
Pfam:AAA_23 7 361 2e-10 PFAM
Pfam:AAA_21 27 372 7.2e-9 PFAM
low complexity region 422 437 N/A INTRINSIC
SMC_hinge 513 629 1.5e-23 SMART
PDB:1W1W|D 1046 1218 3e-42 PDB
Blast:AAA 1063 1217 5e-25 BLAST
SCOP:d1e69a_ 1114 1202 3e-5 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000105085
SMART Domains Protein: ENSMUSP00000100709
Gene: ENSMUSG00000078289

DomainStartEndE-ValueType
Pfam:Ribosomal_L23eN 13 64 1.4e-26 PFAM
Pfam:Ribosomal_L23 72 139 4e-18 PFAM
Meta Mutation Damage Score 0.2977 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 98.0%
  • 10x: 95.3%
  • 20x: 88.9%
Validation Efficiency 100% (80/80)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] SMC1L2 belongs to a family of proteins required for chromatid cohesion and DNA recombination during meiosis and mitosis (3:Revenkova et al., 2001 [PubMed 11564881]).[supplied by OMIM, Mar 2008]
PHENOTYPE: Homozygous mutant mice display male and female infertility, abnormal male and female meiosis, and arrest of spematogenesis. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcd3 T G 3: 121,573,245 (GRCm39) E262D probably damaging Het
Abcg1 G A 17: 31,330,210 (GRCm39) A504T probably benign Het
Acot11 T C 4: 106,606,545 (GRCm39) T515A probably benign Het
Alg8 A T 7: 97,032,891 (GRCm39) probably null Het
Arhgap44 T A 11: 64,917,642 (GRCm39) H375L probably benign Het
Aspm A T 1: 139,384,496 (GRCm39) I98F probably damaging Het
Atp8b5 T C 4: 43,305,719 (GRCm39) probably benign Het
Coa3 T C 11: 101,169,611 (GRCm39) K48R probably damaging Het
Col12a1 A G 9: 79,607,005 (GRCm39) S473P probably damaging Het
Dnmt1 A T 9: 20,833,684 (GRCm39) Y451N probably damaging Het
Dock5 A G 14: 68,043,927 (GRCm39) Y819H possibly damaging Het
Dtx1 G A 5: 120,848,484 (GRCm39) probably benign Het
Dus2 T A 8: 106,780,114 (GRCm39) F479I probably benign Het
Elp1 T C 4: 56,786,723 (GRCm39) T407A probably benign Het
Esrp1 T C 4: 11,365,205 (GRCm39) E262G probably damaging Het
Exoc4 A G 6: 33,418,951 (GRCm39) Y466C probably damaging Het
Fasn A G 11: 120,703,150 (GRCm39) F1625S possibly damaging Het
Fbxw25 A T 9: 109,479,128 (GRCm39) H374Q probably benign Het
Focad T C 4: 88,114,984 (GRCm39) probably benign Het
Gad2 G T 2: 22,571,406 (GRCm39) R448L probably damaging Het
Gad2 G A 2: 22,580,171 (GRCm39) probably benign Het
Galnt16 G T 12: 80,637,405 (GRCm39) E377D probably benign Het
Gcc1 A C 6: 28,419,166 (GRCm39) L389R probably damaging Het
Ggct A T 6: 54,966,554 (GRCm39) probably benign Het
Gm7052 G A 17: 22,259,133 (GRCm39) probably benign Het
Gps2 T A 11: 69,806,507 (GRCm39) H177Q possibly damaging Het
Heg1 T A 16: 33,583,961 (GRCm39) L1256Q probably damaging Het
Il36a G A 2: 24,106,602 (GRCm39) G62E probably damaging Het
Il3ra C T 14: 14,349,317 (GRCm38) R138W probably damaging Het
Itprid1 G T 6: 55,945,245 (GRCm39) K655N probably damaging Het
Kdm4b T A 17: 56,706,430 (GRCm39) I848N probably damaging Het
L3hypdh A G 12: 72,120,770 (GRCm39) V327A possibly damaging Het
Lepr G T 4: 101,628,552 (GRCm39) L552F probably damaging Het
Lpin3 T C 2: 160,740,941 (GRCm39) I449T probably damaging Het
Lrrn1 A G 6: 107,544,225 (GRCm39) K8E probably benign Het
Mex3a G T 3: 88,443,967 (GRCm39) D348Y possibly damaging Het
Mindy2 G A 9: 70,538,361 (GRCm39) R325* probably null Het
Mkrn1 A T 6: 39,376,268 (GRCm39) M382K probably damaging Het
Mroh1 G T 15: 76,330,709 (GRCm39) probably benign Het
Myo15a T A 11: 60,383,892 (GRCm39) D1646E probably damaging Het
Neu2 A G 1: 87,524,450 (GRCm39) D145G probably damaging Het
Obi1 A T 14: 104,717,200 (GRCm39) L391* probably null Het
Or10ah1-ps1 A T 5: 143,123,374 (GRCm39) N216K probably benign Het
Or11g27 T C 14: 50,771,159 (GRCm39) S97P possibly damaging Het
Or2w3b T C 11: 58,623,742 (GRCm39) Y83C probably benign Het
Plekhm2 T A 4: 141,355,295 (GRCm39) I938F probably benign Het
Pnma8a A T 7: 16,695,392 (GRCm39) K416* probably null Het
Ppid T C 3: 79,506,168 (GRCm39) S198P probably benign Het
Rabl6 G T 2: 25,477,538 (GRCm39) P304Q probably damaging Het
Rasal2 A T 1: 157,005,208 (GRCm39) probably benign Het
Ripor1 G T 8: 106,345,560 (GRCm39) probably benign Het
Rnf216 A T 5: 143,054,124 (GRCm39) L658Q probably damaging Het
Safb T A 17: 56,908,228 (GRCm39) probably benign Het
Sf3b5 T C 10: 12,884,497 (GRCm39) M44T probably benign Het
Slc26a9 A T 1: 131,686,536 (GRCm39) M419L probably benign Het
Slc38a8 T C 8: 120,209,394 (GRCm39) D393G probably benign Het
Slc6a3 A G 13: 73,705,199 (GRCm39) D230G probably benign Het
Smg7 G C 1: 152,721,334 (GRCm39) P626R probably damaging Het
Smu1 C T 4: 40,755,722 (GRCm39) V48M probably benign Het
Spag17 T C 3: 99,934,667 (GRCm39) Y650H possibly damaging Het
Spata1 C T 3: 146,181,053 (GRCm39) V302I possibly damaging Het
Sptb G A 12: 76,650,377 (GRCm39) A1780V probably damaging Het
Srrm2 G A 17: 24,038,591 (GRCm39) probably benign Het
Sspo A C 6: 48,474,377 (GRCm39) N4933H probably damaging Het
Sult2a2 T C 7: 13,468,798 (GRCm39) I88T probably benign Het
Tgfa G T 6: 86,247,072 (GRCm39) probably benign Het
Thsd1 T A 8: 22,733,708 (GRCm39) C252S possibly damaging Het
Tmem102 T A 11: 69,695,630 (GRCm39) H114L probably damaging Het
Tnni3k T A 3: 154,498,414 (GRCm39) K808N possibly damaging Het
Trpm7 G T 2: 126,639,713 (GRCm39) L1628M probably benign Het
Ttn A G 2: 76,561,081 (GRCm39) Y29107H probably damaging Het
Upb1 T C 10: 75,273,999 (GRCm39) L342P probably damaging Het
Vmn2r120 T C 17: 57,832,829 (GRCm39) T117A probably benign Het
Vmn2r16 A G 5: 109,487,652 (GRCm39) D175G probably damaging Het
Vps35l A T 7: 118,374,552 (GRCm39) I351F probably damaging Het
Zfhx4 T G 3: 5,464,930 (GRCm39) M1696R possibly damaging Het
Zfp746 A G 6: 48,041,856 (GRCm39) V289A possibly damaging Het
Zfyve26 A C 12: 79,318,901 (GRCm39) F1146V probably damaging Het
Other mutations in Smc1b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00736:Smc1b APN 15 85,013,901 (GRCm39) missense possibly damaging 0.95
IGL01293:Smc1b APN 15 85,016,099 (GRCm39) missense probably damaging 1.00
IGL01656:Smc1b APN 15 84,998,977 (GRCm39) missense probably damaging 0.99
IGL01807:Smc1b APN 15 84,980,946 (GRCm39) missense probably damaging 0.97
IGL02094:Smc1b APN 15 84,982,092 (GRCm39) splice site probably benign
IGL02121:Smc1b APN 15 84,982,186 (GRCm39) missense probably benign
IGL02631:Smc1b APN 15 84,991,204 (GRCm39) missense probably damaging 0.98
IGL02678:Smc1b APN 15 84,949,201 (GRCm39) nonsense probably null
IGL03197:Smc1b APN 15 84,955,064 (GRCm39) missense possibly damaging 0.85
IGL03214:Smc1b APN 15 84,982,147 (GRCm39) nonsense probably null
IGL03218:Smc1b APN 15 84,973,914 (GRCm39) missense probably benign 0.07
IGL03232:Smc1b APN 15 85,013,921 (GRCm39) missense possibly damaging 0.68
adamantine UTSW 15 85,005,842 (GRCm39) missense probably benign 0.06
unbreakable UTSW 15 84,980,859 (GRCm39) missense probably benign
E0370:Smc1b UTSW 15 85,011,782 (GRCm39) missense probably damaging 1.00
PIT4812001:Smc1b UTSW 15 84,953,852 (GRCm39) missense possibly damaging 0.91
R0092:Smc1b UTSW 15 84,951,925 (GRCm39) unclassified probably benign
R0106:Smc1b UTSW 15 84,955,020 (GRCm39) missense probably damaging 1.00
R0106:Smc1b UTSW 15 84,955,020 (GRCm39) missense probably damaging 1.00
R0207:Smc1b UTSW 15 85,007,960 (GRCm39) missense probably benign
R0390:Smc1b UTSW 15 84,950,478 (GRCm39) missense probably damaging 1.00
R0440:Smc1b UTSW 15 84,996,874 (GRCm39) splice site probably benign
R0685:Smc1b UTSW 15 84,955,021 (GRCm39) missense possibly damaging 0.92
R1392:Smc1b UTSW 15 84,991,271 (GRCm39) splice site probably benign
R1509:Smc1b UTSW 15 84,970,335 (GRCm39) missense probably benign
R1804:Smc1b UTSW 15 85,011,991 (GRCm39) missense possibly damaging 0.90
R1879:Smc1b UTSW 15 84,976,268 (GRCm39) missense probably benign 0.01
R2086:Smc1b UTSW 15 85,006,052 (GRCm39) splice site probably benign
R2143:Smc1b UTSW 15 85,008,003 (GRCm39) missense probably benign
R2158:Smc1b UTSW 15 85,006,052 (GRCm39) splice site probably benign
R2174:Smc1b UTSW 15 85,006,052 (GRCm39) splice site probably benign
R2471:Smc1b UTSW 15 84,976,218 (GRCm39) missense probably damaging 0.98
R3689:Smc1b UTSW 15 85,001,464 (GRCm39) intron probably benign
R3690:Smc1b UTSW 15 85,001,464 (GRCm39) intron probably benign
R4178:Smc1b UTSW 15 85,004,848 (GRCm39) missense possibly damaging 0.94
R4420:Smc1b UTSW 15 84,997,031 (GRCm39) missense probably damaging 1.00
R4905:Smc1b UTSW 15 84,950,428 (GRCm39) missense probably damaging 1.00
R4919:Smc1b UTSW 15 85,001,305 (GRCm39) intron probably benign
R5114:Smc1b UTSW 15 84,949,185 (GRCm39) missense probably damaging 1.00
R5314:Smc1b UTSW 15 84,955,066 (GRCm39) missense probably benign 0.00
R5476:Smc1b UTSW 15 84,970,352 (GRCm39) missense probably damaging 0.97
R5593:Smc1b UTSW 15 85,005,842 (GRCm39) missense probably benign 0.06
R5690:Smc1b UTSW 15 84,996,974 (GRCm39) missense probably damaging 1.00
R5719:Smc1b UTSW 15 84,980,859 (GRCm39) missense probably benign
R5817:Smc1b UTSW 15 84,951,984 (GRCm39) missense probably damaging 0.99
R5834:Smc1b UTSW 15 84,973,866 (GRCm39) missense probably damaging 1.00
R5930:Smc1b UTSW 15 84,970,322 (GRCm39) missense probably damaging 1.00
R6032:Smc1b UTSW 15 84,950,430 (GRCm39) missense possibly damaging 0.92
R6032:Smc1b UTSW 15 84,950,430 (GRCm39) missense possibly damaging 0.92
R6049:Smc1b UTSW 15 85,005,896 (GRCm39) missense probably damaging 1.00
R6306:Smc1b UTSW 15 85,011,824 (GRCm39) missense probably benign 0.30
R6392:Smc1b UTSW 15 84,976,232 (GRCm39) missense probably benign 0.03
R6426:Smc1b UTSW 15 84,976,232 (GRCm39) missense probably benign 0.03
R6435:Smc1b UTSW 15 84,976,232 (GRCm39) missense probably benign 0.03
R6436:Smc1b UTSW 15 84,976,232 (GRCm39) missense probably benign 0.03
R6437:Smc1b UTSW 15 84,976,232 (GRCm39) missense probably benign 0.03
R6508:Smc1b UTSW 15 84,976,232 (GRCm39) missense probably benign 0.03
R6512:Smc1b UTSW 15 84,976,232 (GRCm39) missense probably benign 0.03
R6703:Smc1b UTSW 15 84,976,232 (GRCm39) missense probably benign 0.03
R6737:Smc1b UTSW 15 84,976,232 (GRCm39) missense probably benign 0.03
R6775:Smc1b UTSW 15 84,973,881 (GRCm39) missense probably damaging 0.96
R6889:Smc1b UTSW 15 84,951,960 (GRCm39) missense probably damaging 1.00
R6908:Smc1b UTSW 15 84,991,211 (GRCm39) missense probably damaging 1.00
R7124:Smc1b UTSW 15 84,955,798 (GRCm39) missense probably damaging 0.98
R7400:Smc1b UTSW 15 84,953,921 (GRCm39) missense probably damaging 1.00
R7417:Smc1b UTSW 15 84,981,743 (GRCm39) missense probably benign 0.05
R7610:Smc1b UTSW 15 84,955,021 (GRCm39) missense possibly damaging 0.92
R7873:Smc1b UTSW 15 84,994,851 (GRCm39) critical splice donor site probably null
R7890:Smc1b UTSW 15 84,950,529 (GRCm39) missense probably damaging 1.00
R8004:Smc1b UTSW 15 84,981,815 (GRCm39) missense probably damaging 0.98
R8698:Smc1b UTSW 15 84,997,047 (GRCm39) missense probably benign 0.16
R8826:Smc1b UTSW 15 84,950,529 (GRCm39) missense probably damaging 1.00
R8835:Smc1b UTSW 15 85,013,949 (GRCm39) missense possibly damaging 0.83
R8925:Smc1b UTSW 15 84,991,273 (GRCm39) splice site probably null
R9059:Smc1b UTSW 15 85,004,875 (GRCm39) nonsense probably null
R9149:Smc1b UTSW 15 84,950,431 (GRCm39) missense probably benign 0.00
R9241:Smc1b UTSW 15 84,976,209 (GRCm39) missense probably benign 0.00
R9245:Smc1b UTSW 15 85,004,846 (GRCm39) missense probably benign 0.03
R9301:Smc1b UTSW 15 85,011,995 (GRCm39) missense probably damaging 0.98
R9384:Smc1b UTSW 15 84,950,455 (GRCm39) missense probably damaging 0.99
R9750:Smc1b UTSW 15 85,016,106 (GRCm39) missense probably damaging 1.00
Z1176:Smc1b UTSW 15 85,016,104 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CATCCCATAGCTGCCAGTTTGGAG -3'
(R):5'- TCACCTATTGCTTAAAGACGGCACTTG -3'

Sequencing Primer
(F):5'- CTGCCAGTTTGGAGCAATAAAG -3'
(R):5'- TCACTCTATGGGAAAGCAGTC -3'
Posted On 2014-01-05