Incidental Mutation 'R4897:Ldb1'
ID 430216
Institutional Source Beutler Lab
Gene Symbol Ldb1
Ensembl Gene ENSMUSG00000025223
Gene Name LIM domain binding 1
Synonyms CLIM2
MMRRC Submission 042501-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4897 (G1)
Quality Score 225
Status Validated
Chromosome 19
Chromosomal Location 46020009-46033653 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 46023132 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Valine at position 217 (A217V)
Ref Sequence ENSEMBL: ENSMUSP00000139562 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026252] [ENSMUST00000056931] [ENSMUST00000137771] [ENSMUST00000152946] [ENSMUST00000185355] [ENSMUST00000156585]
AlphaFold P70662
Predicted Effect probably benign
Transcript: ENSMUST00000026252
AA Change: A181V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000026252
Gene: ENSMUSG00000025223
AA Change: A181V

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
AA Change: A181V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000053680
Gene: ENSMUSG00000025223
AA Change: A181V

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 noncoding transcript
Transcript: ENSMUST00000126320
Predicted Effect noncoding transcript
Transcript: ENSMUST00000136203
Predicted Effect probably benign
Transcript: ENSMUST00000137771
AA Change: A181V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000114667
Gene: ENSMUSG00000025223
AA Change: A181V

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
AA Change: A181V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000116909
Gene: ENSMUSG00000025223
AA Change: A181V

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 benign
Transcript: ENSMUST00000185355
AA Change: A217V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000139562
Gene: ENSMUSG00000025223
AA Change: A217V

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
Predicted Effect probably benign
Transcript: ENSMUST00000156585
AA Change: A217V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000118546
Gene: ENSMUSG00000025223
AA Change: A217V

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
Meta Mutation Damage Score 0.1139 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.1%
Validation Efficiency 100% (79/79)
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: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930402F06Rik C A 2: 35,266,309 (GRCm39) M120I probably damaging Het
4933427D14Rik A T 11: 72,082,342 (GRCm39) L328Q probably damaging Het
Adgrv1 A C 13: 81,709,704 (GRCm39) probably null Het
Ankrd46 A T 15: 36,484,279 (GRCm39) probably benign Het
Arhgef18 A T 8: 3,494,979 (GRCm39) M413L probably benign Het
Atp6v1e1 G A 6: 120,781,044 (GRCm39) T87M probably null Het
Bap1 T C 14: 30,980,402 (GRCm39) probably benign Het
Brf1 A G 12: 112,929,507 (GRCm39) L385P probably benign Het
C1qtnf1 A T 11: 118,338,938 (GRCm39) N203Y probably damaging Het
Catsperb A T 12: 101,569,025 (GRCm39) N899I probably damaging Het
Ccnjl A C 11: 43,470,718 (GRCm39) D162A probably damaging Het
Cd248 A C 19: 5,119,195 (GRCm39) I348L probably benign Het
Cdc20 T C 4: 118,293,029 (GRCm39) T265A probably benign Het
Cdca5 T A 19: 6,140,427 (GRCm39) L196* probably null Het
Cdk4 T A 10: 126,900,444 (GRCm39) probably benign Het
Cldn10 G A 14: 119,025,725 (GRCm39) G53S possibly damaging Het
Clec4b2 G T 6: 123,177,999 (GRCm39) E105* probably null Het
Dapk1 T A 13: 60,909,600 (GRCm39) D1404E probably benign Het
Dnah1 T C 14: 30,989,496 (GRCm39) Y3308C probably damaging Het
Dnah17 A C 11: 117,969,419 (GRCm39) Y2260D probably damaging Het
Dock8 T G 19: 25,159,001 (GRCm39) S1720A probably benign Het
Erc1 A G 6: 119,754,947 (GRCm39) probably null Het
Ergic1 A G 17: 26,848,597 (GRCm39) I66V probably benign Het
Fam186a T C 15: 99,843,158 (GRCm39) T1029A possibly damaging Het
Fat4 A T 3: 39,034,781 (GRCm39) Y2811F probably damaging Het
Flt3 A G 5: 147,306,110 (GRCm39) M310T probably damaging Het
Ganab T A 19: 8,892,355 (GRCm39) C844S probably benign Het
Gas2l2 C A 11: 83,320,041 (GRCm39) V72F probably damaging Het
Gm14401 T A 2: 176,778,573 (GRCm39) C220S probably damaging Het
Hmmr A T 11: 40,619,261 (GRCm39) V73E probably benign Het
Idi2l T G 13: 8,990,637 (GRCm39) probably benign Het
Ifih1 G T 2: 62,465,358 (GRCm39) probably benign Het
Jak3 A G 8: 72,138,048 (GRCm39) E833G probably damaging Het
Lama2 TTTGCGCATT TTT 10: 26,919,639 (GRCm39) probably null Het
Lrrc8c A G 5: 105,755,955 (GRCm39) T577A probably benign Het
Mfn1 T A 3: 32,600,711 (GRCm39) probably benign Het
Mki67 G A 7: 135,298,474 (GRCm39) P2187S probably damaging Het
Mrc1 T A 2: 14,323,952 (GRCm39) D1096E probably benign Het
Msi1 A G 5: 115,573,654 (GRCm39) probably benign Het
Msto1 T A 3: 88,819,559 (GRCm39) I152F probably benign Het
Myo9a A G 9: 59,803,800 (GRCm39) R2060G probably benign Het
Nnt A T 13: 119,541,107 (GRCm39) C44* probably null Het
Nup210l A G 3: 90,100,378 (GRCm39) D1468G probably damaging Het
Or1j16 T C 2: 36,530,906 (GRCm39) L285P probably damaging Het
Or4c10b A G 2: 89,711,476 (GRCm39) E102G probably benign Het
Or5d46 C A 2: 88,174,686 (GRCm39) C129F possibly damaging Het
Or7a40 T C 16: 16,491,482 (GRCm39) D121G probably damaging Het
P2rx3 G A 2: 84,855,270 (GRCm39) T62I probably damaging Het
Pabpc4l G T 3: 46,401,578 (GRCm39) T22K probably damaging Het
Pcdha7 A G 18: 37,108,646 (GRCm39) D557G probably damaging Het
Pcdhb20 A G 18: 37,639,298 (GRCm39) K608R possibly damaging Het
Pcnx1 A G 12: 81,964,939 (GRCm39) S369G probably damaging Het
Plod1 T C 4: 148,004,736 (GRCm39) I455V probably benign Het
Prune2 A T 19: 17,099,219 (GRCm39) E1574D probably benign Het
Ptar1 T A 19: 23,680,472 (GRCm39) L96H probably damaging Het
Rabgap1 T C 2: 37,450,583 (GRCm39) S904P probably benign Het
Rps6ka4 C T 19: 6,815,467 (GRCm39) V176I probably benign Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Runx1t1 T A 4: 13,771,459 (GRCm39) M1K probably null Het
Serinc4 T A 2: 121,282,905 (GRCm39) Y419F probably damaging Het
Serpina12 A T 12: 104,004,056 (GRCm39) M192K possibly damaging Het
Spata21 T A 4: 140,832,261 (GRCm39) M474K probably damaging Het
Stpg1 T C 4: 135,246,676 (GRCm39) S135P possibly damaging Het
Tdrkh A G 3: 94,336,671 (GRCm39) D481G probably damaging Het
Ube2e1 A C 14: 18,285,268 (GRCm38) S68R probably damaging Het
Vcpip1 A C 1: 9,817,572 (GRCm39) N270K probably damaging Het
Vmn2r79 T C 7: 86,650,675 (GRCm39) F154L probably benign Het
Vwa3b A G 1: 37,153,684 (GRCm39) probably benign Het
Xdh C A 17: 74,207,703 (GRCm39) V885L probably benign Het
Zfp141 A T 7: 42,125,629 (GRCm39) V281D probably benign Het
Zfp317 T A 9: 19,558,143 (GRCm39) I119N probably benign Het
Zfp345 G A 2: 150,314,608 (GRCm39) R310C probably benign Het
Zfp760 G A 17: 21,942,229 (GRCm39) C468Y 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
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
R9742:Ldb1 UTSW 19 46,023,858 (GRCm39) critical splice donor site probably null
X0027:Ldb1 UTSW 19 46,022,528 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- CATGGGCTCTAGTATCACACAG -3'
(R):5'- AGACGTGGCACTTCAGCATC -3'

Sequencing Primer
(F):5'- GCTCTAGTATCACACAGAGCTGG -3'
(R):5'- GCATCCGGCAACACAGAGAG -3'
Posted On 2016-09-21