Incidental Mutation 'R9742:Ldb1'
ID 731902
Institutional Source Beutler Lab
Gene Symbol Ldb1
Ensembl Gene ENSMUSG00000025223
Gene Name LIM domain binding 1
Synonyms CLIM2
MMRRC Submission
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9742 (G1)
Quality Score 217.009
Status Not validated
Chromosome 19
Chromosomal Location 46020009-46033653 bp(-) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) A to G at 46023858 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000118546 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026252] [ENSMUST00000056931] [ENSMUST00000137771] [ENSMUST00000152946] [ENSMUST00000156585] [ENSMUST00000185355]
AlphaFold P70662
Predicted Effect probably benign
Transcript: ENSMUST00000026252
SMART Domains Protein: ENSMUSP00000026252
Gene: ENSMUSG00000025223

DomainStartEndE-ValueType
Pfam:LIM_bind 32 236 1e-72 PFAM
low complexity region 264 287 N/A INTRINSIC
PDB:2JTN|A 295 339 1e-22 PDB
low complexity region 355 368 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000056931
SMART Domains Protein: ENSMUSP00000053680
Gene: ENSMUSG00000025223

DomainStartEndE-ValueType
Pfam:LIM_bind 32 236 1e-72 PFAM
low complexity region 264 287 N/A INTRINSIC
PDB:2JTN|A 295 339 1e-22 PDB
low complexity region 355 368 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000137771
SMART Domains Protein: ENSMUSP00000114667
Gene: ENSMUSG00000025223

DomainStartEndE-ValueType
Pfam:LIM_bind 32 236 5.4e-73 PFAM
low complexity region 264 287 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000152946
SMART Domains Protein: ENSMUSP00000116909
Gene: ENSMUSG00000025223

DomainStartEndE-ValueType
Pfam:LIM_bind 33 189 1.1e-42 PFAM
Pfam:LIM_bind 178 235 5.5e-15 PFAM
low complexity region 264 287 N/A INTRINSIC
PDB:2YPA|D 298 337 4e-21 PDB
low complexity region 353 366 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000156585
SMART Domains Protein: ENSMUSP00000118546
Gene: ENSMUSG00000025223

DomainStartEndE-ValueType
Pfam:LIM_bind 69 225 5.9e-42 PFAM
Pfam:LIM_bind 214 271 2.5e-14 PFAM
low complexity region 300 323 N/A INTRINSIC
PDB:2JTN|A 331 375 2e-22 PDB
low complexity region 391 404 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000185355
SMART Domains Protein: ENSMUSP00000139562
Gene: ENSMUSG00000025223

DomainStartEndE-ValueType
Pfam:LIM_bind 68 272 5.6e-73 PFAM
low complexity region 300 323 N/A INTRINSIC
PDB:2JTN|A 331 375 2e-22 PDB
low complexity region 391 404 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 99.3%
  • 20x: 98.1%
Validation Efficiency
MGI Phenotype PHENOTYPE: Mice homozygous for disruptions in this gene die as embryos at E9.5-E10 with impaired primitive erythropoiesis and vascular development. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acan T G 7: 78,749,115 (GRCm39) S1295R probably benign Het
Acsf2 C A 11: 94,463,963 (GRCm39) V74L probably benign Het
Actrt3 T C 3: 30,652,434 (GRCm39) Y220C probably damaging Het
Adgrl2 A G 3: 148,541,986 (GRCm39) probably null Het
Ak2 T A 4: 128,901,961 (GRCm39) D211E possibly damaging Het
Atp4b G A 8: 13,440,097 (GRCm39) T83I probably damaging Het
Brat1 A G 5: 140,703,912 (GRCm39) T722A probably benign Het
Cfap65 T C 1: 74,943,840 (GRCm39) Y1557C probably benign Het
Cmya5 T C 13: 93,231,935 (GRCm39) D1051G possibly damaging Het
Cuedc2 A G 19: 46,319,727 (GRCm39) probably null Het
Dtnb A T 12: 3,736,740 (GRCm39) K293N possibly damaging Het
Dusp26 A T 8: 31,584,198 (GRCm39) T102S probably benign Het
Epg5 T A 18: 78,024,170 (GRCm39) L1079H probably damaging Het
Epha6 T C 16: 60,026,065 (GRCm39) Y459C probably damaging Het
Fam89b A T 19: 5,779,330 (GRCm39) S76T probably benign Het
Fbxo33 A G 12: 59,251,682 (GRCm39) S278P probably damaging Het
Fndc3a C A 14: 72,777,693 (GRCm39) E1171* probably null Het
Grip1 G A 10: 119,874,569 (GRCm39) E778K possibly damaging Het
Il17ra T A 6: 120,458,466 (GRCm39) I539N probably damaging Het
Khdc1c T G 1: 21,439,945 (GRCm39) H165Q probably benign Het
Lrrc27 C T 7: 138,806,229 (GRCm39) A298V probably benign Het
Lsr CTCTTCTTCTTCTTCTTC CTCTTCTTCTTCTTC 7: 30,657,492 (GRCm39) probably benign Het
Mpi A G 9: 57,452,606 (GRCm39) C309R probably damaging Het
Mrtfa G A 15: 80,901,180 (GRCm39) A472V possibly damaging Het
Mtcl3 C A 10: 29,024,394 (GRCm39) Q437K probably benign Het
Muc17 A G 5: 137,167,127 (GRCm39) Y276H Het
Myh6 T A 14: 55,194,056 (GRCm39) M778L probably benign Het
Nmnat1 T A 4: 149,553,338 (GRCm39) E258V probably damaging Het
Or10ag53 T C 2: 87,082,376 (GRCm39) F32L probably benign Het
Or5b108 T C 19: 13,168,769 (GRCm39) V246A probably damaging Het
Pik3c2b A G 1: 133,022,487 (GRCm39) E1143G probably damaging Het
Plch2 C T 4: 155,082,912 (GRCm39) D579N probably damaging Het
Slc22a19 T C 19: 7,688,281 (GRCm39) Q93R probably benign Het
Slc9c1 T A 16: 45,400,616 (GRCm39) I742N probably damaging Het
Smarcc2 A G 10: 128,297,222 (GRCm39) Y38C probably damaging Het
Strbp T C 2: 37,515,268 (GRCm39) T253A probably damaging Het
Trim40 A G 17: 37,199,902 (GRCm39) S59P possibly damaging Het
Trpm6 G T 19: 18,800,766 (GRCm39) V827L probably benign Het
Unc5d A G 8: 29,156,792 (GRCm39) probably null Het
Vmn2r118 T C 17: 55,918,009 (GRCm39) T168A probably damaging Het
Wdfy4 G A 14: 32,809,987 (GRCm39) H1745Y Het
Xrra1 A G 7: 99,563,660 (GRCm39) D549G probably benign Het
Zhx2 A G 15: 57,686,806 (GRCm39) E725G probably benign Het
Zzef1 G A 11: 72,749,179 (GRCm39) R889H probably benign Het
Other mutations in Ldb1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01603:Ldb1 APN 19 46,024,014 (GRCm39) missense probably damaging 1.00
IGL02069:Ldb1 APN 19 46,021,617 (GRCm39) missense possibly damaging 0.88
IGL02380:Ldb1 APN 19 46,022,929 (GRCm39) missense possibly damaging 0.95
IGL02441:Ldb1 APN 19 46,024,195 (GRCm39) missense probably damaging 0.99
IGL02677:Ldb1 APN 19 46,024,594 (GRCm39) splice site probably benign
R1585:Ldb1 UTSW 19 46,022,903 (GRCm39) missense probably damaging 0.99
R3720:Ldb1 UTSW 19 46,033,331 (GRCm39) start gained probably benign
R4897:Ldb1 UTSW 19 46,023,132 (GRCm39) missense probably benign
R5830:Ldb1 UTSW 19 46,022,557 (GRCm39) missense probably benign 0.00
R7663:Ldb1 UTSW 19 46,023,963 (GRCm39) missense probably damaging 1.00
R8482:Ldb1 UTSW 19 46,024,709 (GRCm39) missense probably null 0.99
R8887:Ldb1 UTSW 19 46,023,294 (GRCm39) missense probably damaging 1.00
X0027:Ldb1 UTSW 19 46,022,528 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- TTCACCATATACCTCGGGGC -3'
(R):5'- CTGGAAGTGTGAAGGGTACGTC -3'

Sequencing Primer
(F):5'- TCGGGGCCCAGAAAACTGAC -3'
(R):5'- GAAGGGTACGTCTTGGTCC -3'
Posted On 2022-11-14