Incidental Mutation 'R5039:Kdm1b'
ID 395721
Institutional Source Beutler Lab
Gene Symbol Kdm1b
Ensembl Gene ENSMUSG00000038080
Gene Name lysine (K)-specific demethylase 1B
Synonyms Aof1, 4632428N09Rik
MMRRC Submission 042629-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.504) question?
Stock # R5039 (G1)
Quality Score 225
Status Validated
Chromosome 13
Chromosomal Location 47196849-47238085 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 47230962 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glycine to Aspartic acid at position 663 (G663D)
Ref Sequence ENSEMBL: ENSMUSP00000038373 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000037025]
AlphaFold Q8CIG3
Predicted Effect probably damaging
Transcript: ENSMUST00000037025
AA Change: G663D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: G663D

DomainStartEndE-ValueType
Pfam:zf-CW 138 191 2.6e-13 PFAM
low complexity region 235 253 N/A INTRINSIC
Pfam:SWIRM 286 369 6e-12 PFAM
Pfam:Pyr_redox_2 368 490 3.1e-8 PFAM
Pfam:Thi4 375 446 2.2e-10 PFAM
Pfam:FAD_binding_3 388 423 4.1e-7 PFAM
Pfam:HI0933_like 389 428 1.6e-7 PFAM
Pfam:FAD_binding_2 390 428 1.6e-6 PFAM
Pfam:Pyr_redox 390 438 8e-8 PFAM
Pfam:NAD_binding_8 393 460 1.6e-13 PFAM
Pfam:Amino_oxidase 398 824 3.7e-86 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128977
Predicted Effect unknown
Transcript: ENSMUST00000143518
AA Change: G279D
SMART Domains Protein: ENSMUSP00000114999
Gene: ENSMUSG00000038080
AA Change: G279D

DomainStartEndE-ValueType
Pfam:SWIRM 3 86 1.1e-12 PFAM
Pfam:Thi4 91 163 3.5e-10 PFAM
Pfam:FAD_binding_3 105 140 3.5e-7 PFAM
Pfam:HI0933_like 106 145 1.7e-7 PFAM
Pfam:Pyr_redox_2 106 251 1.5e-10 PFAM
Pfam:FAD_binding_2 107 150 5.7e-7 PFAM
Pfam:Pyr_redox 107 158 6.4e-8 PFAM
Pfam:Pyr_redox_3 109 288 1.2e-13 PFAM
Pfam:NAD_binding_8 110 177 2.3e-13 PFAM
Pfam:Amino_oxidase 115 181 8.6e-19 PFAM
Pfam:Amino_oxidase 178 441 4.5e-63 PFAM
Meta Mutation Damage Score 0.2581 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.5%
Validation Efficiency 100% (61/61)
MGI Phenotype PHENOTYPE: Homozygous null mice of both sexes are viable, grossly normal and male mice are fertile; however, heterozygous progeny of homozygous null mothers display severe placental defects, embryonic growth impairment, neural tube defects and pericardial edema, and do not survive past E10.5. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcg4 G A 9: 44,192,863 (GRCm39) A161V probably damaging Het
Anapc2 T C 2: 25,164,808 (GRCm39) I64T possibly damaging Het
Arfgef1 T C 1: 10,269,961 (GRCm39) D396G probably benign Het
Ark2c A G 18: 77,550,608 (GRCm39) S107P probably damaging Het
Axl C T 7: 25,485,340 (GRCm39) V163M probably damaging Het
Blm G A 7: 80,155,621 (GRCm39) P353S possibly damaging Het
Btaf1 T C 19: 36,968,162 (GRCm39) Y1116H probably benign Het
Ccdc18 T A 5: 108,306,514 (GRCm39) probably null Het
Ccdc87 T C 19: 4,890,429 (GRCm39) probably null Het
Cdhr1 T C 14: 36,801,600 (GRCm39) N781S probably benign Het
Ctr9 C A 7: 110,642,064 (GRCm39) H297Q probably benign Het
Cyp2c55 A G 19: 39,026,587 (GRCm39) D398G probably benign Het
Dnase1l1 C T X: 73,320,644 (GRCm39) probably null Het
Dnmt3l T C 10: 77,888,734 (GRCm39) probably null Het
Dock4 C A 12: 40,867,745 (GRCm39) N1440K probably damaging Het
Etnk1 T A 6: 143,141,043 (GRCm39) probably null Het
Fam120a A T 13: 49,063,726 (GRCm39) probably null Het
Fanca T C 8: 124,010,785 (GRCm39) D908G probably benign Het
Gm17535 T A 9: 3,035,786 (GRCm39) L218H probably benign Het
Gm3633 A C 14: 42,461,161 (GRCm39) N42K possibly damaging Het
Gm4781 C A 10: 100,232,851 (GRCm39) noncoding transcript Het
Gm8741 G T 17: 35,555,062 (GRCm39) noncoding transcript Het
Gpr139 A G 7: 118,744,165 (GRCm39) V140A probably benign Het
Ighv1-62-3 G T 12: 115,425,014 (GRCm39) T13K probably benign Het
Itgb2l T C 16: 96,226,205 (GRCm39) T629A possibly damaging Het
Kcnb2 T C 1: 15,779,724 (GRCm39) S199P probably damaging Het
Lama1 A G 17: 68,052,888 (GRCm39) D407G possibly damaging Het
Macf1 T C 4: 123,405,013 (GRCm39) K391R probably damaging Het
Magi3 A T 3: 104,013,107 (GRCm39) S127T probably damaging Het
Map2 A T 1: 66,477,955 (GRCm39) D1759V probably damaging Het
Mllt6 G A 11: 97,560,326 (GRCm39) S210N possibly damaging Het
Myrfl T C 10: 116,658,616 (GRCm39) D447G probably damaging Het
Ndufb7 A G 8: 84,298,094 (GRCm39) probably benign Het
Nt5e T A 9: 88,245,634 (GRCm39) N301K probably benign Het
Or10d4b A T 9: 39,534,856 (GRCm39) T146S possibly damaging Het
Or8g27 T A 9: 39,129,410 (GRCm39) Y252* probably null Het
Pcdh10 A G 3: 45,336,296 (GRCm39) N870S probably damaging Het
Pcdh18 A G 3: 49,709,305 (GRCm39) V670A probably benign Het
Phf8-ps A C 17: 33,286,734 (GRCm39) C23G probably damaging Het
Polr1c G T 17: 46,558,635 (GRCm39) probably benign Het
Ric3 G C 7: 108,637,930 (GRCm39) S274R probably benign Het
Rimbp3 A G 16: 17,031,195 (GRCm39) T1540A probably damaging Het
Rp1l1 A T 14: 64,268,805 (GRCm39) M1464L probably benign Het
Slc41a3 A G 6: 90,603,399 (GRCm39) Y140C probably damaging Het
Ssb A T 2: 69,696,581 (GRCm39) E38D possibly damaging Het
Syt14 A T 1: 192,709,292 (GRCm39) I16N probably damaging Het
Tet3 T C 6: 83,352,878 (GRCm39) T973A probably damaging Het
Tial1 T C 7: 128,045,692 (GRCm39) probably benign Het
Tnfrsf1a A G 6: 125,337,675 (GRCm39) T89A possibly damaging Het
Trpv5 T C 6: 41,652,879 (GRCm39) Y98C possibly damaging Het
Ylpm1 T A 12: 85,062,267 (GRCm39) S265T probably damaging Het
Ylpm1 A G 12: 85,089,013 (GRCm39) D1006G probably damaging Het
Other mutations in Kdm1b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00587:Kdm1b APN 13 47,222,016 (GRCm39) missense probably benign 0.01
IGL00924:Kdm1b APN 13 47,221,956 (GRCm39) missense probably benign
IGL01553:Kdm1b APN 13 47,234,024 (GRCm39) missense probably damaging 0.96
IGL01663:Kdm1b APN 13 47,227,213 (GRCm39) missense probably damaging 0.99
IGL02385:Kdm1b APN 13 47,221,982 (GRCm39) missense possibly damaging 0.49
IGL02505:Kdm1b APN 13 47,214,331 (GRCm39) missense probably damaging 1.00
IGL02826:Kdm1b APN 13 47,233,943 (GRCm39) missense probably damaging 1.00
IGL03257:Kdm1b APN 13 47,202,742 (GRCm39) missense probably damaging 1.00
R0052:Kdm1b UTSW 13 47,217,593 (GRCm39) missense probably damaging 1.00
R0319:Kdm1b UTSW 13 47,207,195 (GRCm39) missense probably benign
R0426:Kdm1b UTSW 13 47,217,720 (GRCm39) splice site probably benign
R0599:Kdm1b UTSW 13 47,212,286 (GRCm39) missense possibly damaging 0.47
R0764:Kdm1b UTSW 13 47,222,079 (GRCm39) missense possibly damaging 0.70
R1163:Kdm1b UTSW 13 47,225,398 (GRCm39) missense probably benign 0.02
R1543:Kdm1b UTSW 13 47,221,997 (GRCm39) missense probably damaging 0.99
R1584:Kdm1b UTSW 13 47,217,530 (GRCm39) missense probably damaging 1.00
R1627:Kdm1b UTSW 13 47,217,707 (GRCm39) critical splice donor site probably null
R1669:Kdm1b UTSW 13 47,222,024 (GRCm39) missense probably damaging 1.00
R1758:Kdm1b UTSW 13 47,214,244 (GRCm39) missense probably benign 0.00
R1860:Kdm1b UTSW 13 47,202,666 (GRCm39) missense probably benign 0.03
R1907:Kdm1b UTSW 13 47,217,596 (GRCm39) missense probably benign 0.00
R2225:Kdm1b UTSW 13 47,217,564 (GRCm39) frame shift probably null
R2239:Kdm1b UTSW 13 47,227,231 (GRCm39) missense probably damaging 1.00
R2271:Kdm1b UTSW 13 47,217,564 (GRCm39) frame shift probably null
R2302:Kdm1b UTSW 13 47,217,564 (GRCm39) frame shift probably null
R2303:Kdm1b UTSW 13 47,217,564 (GRCm39) frame shift probably null
R2380:Kdm1b UTSW 13 47,227,231 (GRCm39) missense probably damaging 1.00
R2442:Kdm1b UTSW 13 47,216,451 (GRCm39) missense probably benign 0.32
R3022:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R3054:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R3545:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R3546:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R3548:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R4094:Kdm1b UTSW 13 47,216,496 (GRCm39) missense probably damaging 1.00
R4419:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R4420:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R4502:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R4547:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R4548:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R4785:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R4793:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R4804:Kdm1b UTSW 13 47,216,553 (GRCm39) missense probably damaging 1.00
R4882:Kdm1b UTSW 13 47,214,369 (GRCm39) missense probably benign
R4906:Kdm1b UTSW 13 47,216,620 (GRCm39) critical splice donor site probably null
R4965:Kdm1b UTSW 13 47,227,843 (GRCm39) missense probably damaging 0.98
R5098:Kdm1b UTSW 13 47,216,467 (GRCm39) missense probably damaging 1.00
R5265:Kdm1b UTSW 13 47,216,445 (GRCm39) missense probably benign 0.35
R5541:Kdm1b UTSW 13 47,232,672 (GRCm39) missense probably damaging 1.00
R5814:Kdm1b UTSW 13 47,216,622 (GRCm39) splice site probably null
R6046:Kdm1b UTSW 13 47,232,729 (GRCm39) missense possibly damaging 0.92
R6798:Kdm1b UTSW 13 47,222,012 (GRCm39) missense probably benign 0.00
R6903:Kdm1b UTSW 13 47,227,880 (GRCm39) missense probably benign 0.00
R7831:Kdm1b UTSW 13 47,204,098 (GRCm39) missense probably benign 0.17
R7973:Kdm1b UTSW 13 47,230,922 (GRCm39) missense probably benign 0.00
R8181:Kdm1b UTSW 13 47,205,377 (GRCm39) critical splice donor site probably null
R8248:Kdm1b UTSW 13 47,225,354 (GRCm39) intron probably benign
R8821:Kdm1b UTSW 13 47,217,617 (GRCm39) missense possibly damaging 0.94
R8831:Kdm1b UTSW 13 47,217,617 (GRCm39) missense possibly damaging 0.94
R8842:Kdm1b UTSW 13 47,231,832 (GRCm39) missense probably damaging 1.00
R8861:Kdm1b UTSW 13 47,217,582 (GRCm39) missense probably benign 0.02
R8885:Kdm1b UTSW 13 47,207,184 (GRCm39) nonsense probably null
R9038:Kdm1b UTSW 13 47,202,770 (GRCm39) missense probably benign 0.07
R9132:Kdm1b UTSW 13 47,225,458 (GRCm39) missense probably benign 0.05
R9268:Kdm1b UTSW 13 47,217,705 (GRCm39) missense probably benign 0.00
R9616:Kdm1b UTSW 13 47,234,030 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GGTTTTACGACTGCAAGCAGAG -3'
(R):5'- CTGAATTGGATATCTGACAGCTCATAC -3'

Sequencing Primer
(F):5'- ATAGTCAGGGCTGGTATGAGC -3'
(R):5'- TCTGACAGCTCATACATGTATAGAG -3'
Posted On 2016-06-21