Incidental Mutation 'R6401:Ldb3'
ID 516174
Institutional Source Beutler Lab
Gene Symbol Ldb3
Ensembl Gene ENSMUSG00000021798
Gene Name LIM domain binding 3
Synonyms ZASP, cypher
MMRRC Submission 044548-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6401 (G1)
Quality Score 225.009
Status Validated
Chromosome 14
Chromosomal Location 34248560-34310639 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 34299291 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 111 (L111Q)
Ref Sequence ENSEMBL: ENSMUSP00000022330 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000022327] [ENSMUST00000022328] [ENSMUST00000022330] [ENSMUST00000064098] [ENSMUST00000090040] [ENSMUST00000227819] [ENSMUST00000228044]
AlphaFold Q9JKS4
Predicted Effect probably benign
Transcript: ENSMUST00000022327
AA Change: L111Q

PolyPhen 2 Score 0.329 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000022327
Gene: ENSMUSG00000021798
AA Change: L111Q

DomainStartEndE-ValueType
PDZ 11 84 1.68e-16 SMART
low complexity region 138 147 N/A INTRINSIC
ZM 186 211 1.33e-8 SMART
low complexity region 214 229 N/A INTRINSIC
low complexity region 309 353 N/A INTRINSIC
low complexity region 359 376 N/A INTRINSIC
low complexity region 418 473 N/A INTRINSIC
LIM 546 597 2.72e-16 SMART
LIM 605 656 2.65e-19 SMART
LIM 664 717 1.04e-17 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000022328
AA Change: L111Q

PolyPhen 2 Score 0.329 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000022328
Gene: ENSMUSG00000021798
AA Change: L111Q

DomainStartEndE-ValueType
PDZ 11 84 1.68e-16 SMART
low complexity region 138 147 N/A INTRINSIC
ZM 186 211 1.33e-8 SMART
low complexity region 214 229 N/A INTRINSIC
low complexity region 297 314 N/A INTRINSIC
low complexity region 356 411 N/A INTRINSIC
LIM 484 535 2.72e-16 SMART
LIM 543 594 2.65e-19 SMART
LIM 602 655 1.04e-17 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000022330
AA Change: L111Q

PolyPhen 2 Score 0.329 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000022330
Gene: ENSMUSG00000021798
AA Change: L111Q

DomainStartEndE-ValueType
PDZ 11 84 1.68e-16 SMART
low complexity region 138 147 N/A INTRINSIC
ZM 186 211 1.33e-8 SMART
low complexity region 214 229 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000064098
SMART Domains Protein: ENSMUSP00000066784
Gene: ENSMUSG00000021798

DomainStartEndE-ValueType
PDZ 11 84 1.68e-16 SMART
ZM 148 173 5.18e-11 SMART
low complexity region 265 309 N/A INTRINSIC
low complexity region 315 332 N/A INTRINSIC
low complexity region 374 429 N/A INTRINSIC
LIM 502 553 2.72e-16 SMART
LIM 561 612 2.65e-19 SMART
LIM 620 673 1.04e-17 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000090040
SMART Domains Protein: ENSMUSP00000087494
Gene: ENSMUSG00000021798

DomainStartEndE-ValueType
PDZ 11 84 1.68e-16 SMART
ZM 148 173 5.18e-11 SMART
low complexity region 270 314 N/A INTRINSIC
low complexity region 320 337 N/A INTRINSIC
low complexity region 379 434 N/A INTRINSIC
LIM 507 558 2.72e-16 SMART
LIM 566 617 2.65e-19 SMART
LIM 625 678 1.04e-17 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000226226
Predicted Effect probably benign
Transcript: ENSMUST00000227819
Predicted Effect probably benign
Transcript: ENSMUST00000228044
Meta Mutation Damage Score 0.1125 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.4%
  • 20x: 97.9%
Validation Efficiency 93% (41/44)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. The protein encoded by this gene interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. This protein also interacts with all three members of the myozenin family. Mutations in this gene have been associated with myofibrillar myopathy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding different isoforms have been identified; all isoforms have N-terminal PDZ domains while only longer isoforms (1, 2 and 5) have C-terminal LIM domains. [provided by RefSeq, Jan 2010]
PHENOTYPE: Homozygous mutation of this gene results in lethality within a few days after birth from muscle abnormalities. Mutant mice exhibit myopathy, dysphagia, heart vascular congestion, dilated heart ventricles, cyanosis, and respiratory distress. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 41 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ano3 T A 2: 110,605,459 (GRCm39) N249I probably benign Het
Ap3s1 A C 18: 46,891,074 (GRCm39) I56L probably benign Het
Ccn5 T C 2: 163,670,946 (GRCm39) I151T probably benign Het
Cngb1 A G 8: 96,030,367 (GRCm39) probably benign Het
Col2a1 T C 15: 97,883,773 (GRCm39) T570A unknown Het
Cyp3a16 T C 5: 145,377,174 (GRCm39) E471G probably damaging Het
D930020B18Rik A G 10: 121,477,762 (GRCm39) N14D possibly damaging Het
Ext1 T C 15: 52,969,493 (GRCm39) E365G possibly damaging Het
Fbn1 C A 2: 125,188,370 (GRCm39) V1490F probably damaging Het
Fsip2 A G 2: 82,820,430 (GRCm39) T5388A possibly damaging Het
Gm5431 T A 11: 48,779,536 (GRCm39) N740I probably benign Het
Ifi209 T C 1: 173,472,269 (GRCm39) M370T probably damaging Het
Ighv2-4 G T 12: 113,617,082 (GRCm39) P60Q probably damaging Het
Kif19b A T 5: 140,442,698 (GRCm39) T80S possibly damaging Het
Mcmbp G T 7: 128,308,783 (GRCm39) L413I possibly damaging Het
Mib1 T A 18: 10,795,802 (GRCm39) M721K probably benign Het
Nos3 A G 5: 24,584,809 (GRCm39) T738A probably benign Het
Notch3 T A 17: 32,377,597 (GRCm39) I160L probably benign Het
Nrxn3 C A 12: 89,221,770 (GRCm39) N516K possibly damaging Het
Nt5c2 A G 19: 46,878,250 (GRCm39) Y496H probably benign Het
Or13f5 A C 4: 52,826,242 (GRCm39) T282P probably damaging Het
Or1n1 A T 2: 36,750,177 (GRCm39) L61* probably null Het
Or5b111 T C 19: 13,290,878 (GRCm39) Y257C probably damaging Het
Polm A T 11: 5,779,491 (GRCm39) W436R probably damaging Het
Prex2 T A 1: 11,256,951 (GRCm39) I1221N probably benign Het
Rfpl4b T C 10: 38,696,941 (GRCm39) H220R possibly damaging Het
Rgs12 T C 5: 35,177,676 (GRCm39) F79L probably damaging Het
Rxfp2 A G 5: 149,966,595 (GRCm39) D111G probably benign Het
Smg7 A G 1: 152,715,887 (GRCm39) probably null Het
Spata22 T C 11: 73,224,180 (GRCm39) S34P probably damaging Het
St7 T A 6: 17,855,317 (GRCm39) probably null Het
Stk31 A G 6: 49,400,372 (GRCm39) E399G probably damaging Het
Tcp10b C A 17: 13,292,466 (GRCm39) N296K probably damaging Het
Tonsl T C 15: 76,517,866 (GRCm39) Y645C probably damaging Het
Ttn A T 2: 76,800,206 (GRCm39) M334K probably benign Het
Vcpkmt C A 12: 69,629,619 (GRCm39) V48F probably damaging Het
Vmn2r112 T A 17: 22,822,532 (GRCm39) Y403* probably null Het
Vwa7 G A 17: 35,236,286 (GRCm39) probably null Het
Wscd2 A T 5: 113,726,206 (GRCm39) *572C probably null Het
Xpo7 A G 14: 70,919,787 (GRCm39) L676P probably damaging Het
Zbtb32 A C 7: 30,291,244 (GRCm39) L17W probably damaging Het
Other mutations in Ldb3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01124:Ldb3 APN 14 34,266,157 (GRCm39) missense probably damaging 0.99
IGL01485:Ldb3 APN 14 34,264,519 (GRCm39) missense probably damaging 1.00
IGL01983:Ldb3 APN 14 34,299,156 (GRCm39) missense probably benign 0.00
R0323:Ldb3 UTSW 14 34,266,002 (GRCm39) missense probably damaging 1.00
R0335:Ldb3 UTSW 14 34,300,608 (GRCm39) missense possibly damaging 0.77
R0483:Ldb3 UTSW 14 34,258,541 (GRCm39) missense probably damaging 1.00
R0920:Ldb3 UTSW 14 34,289,460 (GRCm39) missense probably benign 0.05
R1524:Ldb3 UTSW 14 34,277,313 (GRCm39) missense probably benign 0.01
R2161:Ldb3 UTSW 14 34,289,353 (GRCm39) critical splice donor site probably null
R2246:Ldb3 UTSW 14 34,251,432 (GRCm39) missense probably damaging 0.99
R2865:Ldb3 UTSW 14 34,251,460 (GRCm39) missense probably damaging 1.00
R3113:Ldb3 UTSW 14 34,251,418 (GRCm39) makesense probably null
R3765:Ldb3 UTSW 14 34,300,639 (GRCm39) splice site probably null
R3870:Ldb3 UTSW 14 34,289,440 (GRCm39) missense probably damaging 1.00
R4018:Ldb3 UTSW 14 34,274,128 (GRCm39) splice site probably benign
R4797:Ldb3 UTSW 14 34,277,470 (GRCm39) missense possibly damaging 0.95
R4963:Ldb3 UTSW 14 34,288,815 (GRCm39) missense probably damaging 0.98
R5705:Ldb3 UTSW 14 34,298,986 (GRCm39) missense probably null 0.01
R6549:Ldb3 UTSW 14 34,263,854 (GRCm39) missense probably damaging 0.99
R6682:Ldb3 UTSW 14 34,274,221 (GRCm39) missense possibly damaging 0.77
R6917:Ldb3 UTSW 14 34,277,321 (GRCm39) missense probably null 0.03
R7132:Ldb3 UTSW 14 34,298,992 (GRCm39) missense probably benign 0.25
R7327:Ldb3 UTSW 14 34,293,759 (GRCm39) missense probably damaging 1.00
R7488:Ldb3 UTSW 14 34,289,402 (GRCm39) missense probably damaging 1.00
R7760:Ldb3 UTSW 14 34,264,460 (GRCm39) missense probably damaging 1.00
R8755:Ldb3 UTSW 14 34,299,256 (GRCm39) missense probably damaging 1.00
R8845:Ldb3 UTSW 14 34,258,634 (GRCm39) missense probably damaging 1.00
R8954:Ldb3 UTSW 14 34,277,301 (GRCm39) missense probably null 0.17
R9179:Ldb3 UTSW 14 34,277,312 (GRCm39) missense probably benign
R9321:Ldb3 UTSW 14 34,266,099 (GRCm39) nonsense probably null
R9702:Ldb3 UTSW 14 34,299,090 (GRCm39) missense probably benign 0.03
Z1176:Ldb3 UTSW 14 34,277,322 (GRCm39) missense probably benign 0.21
Z1177:Ldb3 UTSW 14 34,266,060 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- GAACTTTGGGGCTGACTGAG -3'
(R):5'- TCTAGACCAGGAGCCACAAG -3'

Sequencing Primer
(F):5'- TGACTGAGCCCTGTGCAC -3'
(R):5'- AGGCCTTCCTTTCCTGTGC -3'
Posted On 2018-05-04