Incidental Mutation 'R9179:Ldb3'
ID 696910
Institutional Source Beutler Lab
Gene Symbol Ldb3
Ensembl Gene ENSMUSG00000021798
Gene Name LIM domain binding 3
Synonyms ZASP, cypher
MMRRC Submission
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9179 (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 34277312 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 354 (V354E)
Ref Sequence ENSEMBL: ENSMUSP00000022327 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000022327] [ENSMUST00000022328] [ENSMUST00000064098] [ENSMUST00000090040] [ENSMUST00000228044]
AlphaFold Q9JKS4
PDB Structure Solution structure of PDZ domain of mouse Cypher protein [SOLUTION NMR]
Predicted Effect probably benign
Transcript: ENSMUST00000022327
AA Change: V354E

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000022327
Gene: ENSMUSG00000021798
AA Change: V354E

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
SMART Domains Protein: ENSMUSP00000022328
Gene: ENSMUSG00000021798

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: ENSMUST00000064098
AA Change: V310E

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000066784
Gene: ENSMUSG00000021798
AA Change: V310E

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
AA Change: V315E

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000087494
Gene: ENSMUSG00000021798
AA Change: V315E

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 probably benign
Transcript: ENSMUST00000228044
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency 98% (54/55)
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700013D24Rik T A 6: 124,333,882 (GRCm39) M33L probably benign Het
2310003L06Rik A G 5: 88,119,890 (GRCm39) T216A probably benign Het
9330161L09Rik A C 12: 103,373,837 (GRCm39) C12G unknown Het
Ahdc1 T A 4: 132,788,929 (GRCm39) F57I possibly damaging Het
Amotl1 C A 9: 14,461,787 (GRCm39) A809S possibly damaging Het
Ankfn1 C T 11: 89,414,011 (GRCm39) M121I probably benign Het
Aspm A G 1: 139,404,453 (GRCm39) D1261G probably damaging Het
Axl T C 7: 25,469,658 (GRCm39) T502A probably damaging Het
Catsperd G A 17: 56,968,252 (GRCm39) D546N probably benign Het
Ccdc102a A G 8: 95,639,748 (GRCm39) V182A possibly damaging Het
Cdh23 C T 10: 60,153,664 (GRCm39) A2309T probably benign Het
Cfap69 A T 5: 5,676,064 (GRCm39) N210K probably benign Het
Cnot1 A G 8: 96,500,054 (GRCm39) S147P probably benign Het
Cntnap5c T C 17: 58,600,912 (GRCm39) S752P probably benign Het
Cyp3a41a A T 5: 145,642,654 (GRCm39) M235K probably benign Het
Cyp4f15 A G 17: 32,919,185 (GRCm39) D336G possibly damaging Het
Dagla A G 19: 10,228,525 (GRCm39) I631T possibly damaging Het
Dph6 C T 2: 114,353,591 (GRCm39) C199Y probably damaging Het
Ermard T A 17: 15,273,495 (GRCm39) L360Q probably damaging Het
F830045P16Rik T C 2: 129,314,708 (GRCm39) T190A probably benign Het
Fgfr3 G T 5: 33,887,316 (GRCm39) V212L possibly damaging Het
Flnb C A 14: 7,887,541 (GRCm38) C450* probably null Het
Gls T C 1: 52,239,015 (GRCm39) Y362C probably damaging Het
Gngt1 A G 6: 3,994,246 (GRCm39) D8G possibly damaging Het
Gns T C 10: 121,216,080 (GRCm39) F276L Het
Grin2d A G 7: 45,506,176 (GRCm39) S572P probably damaging Het
Impa2 C T 18: 67,422,473 (GRCm39) probably benign Het
Itgal A T 7: 126,905,883 (GRCm39) D355V probably benign Het
Kdm6b A T 11: 69,297,521 (GRCm39) probably null Het
Klk1b1 T A 7: 43,618,715 (GRCm39) C31S probably damaging Het
Mettl21c T A 1: 44,049,142 (GRCm39) Y135F probably benign Het
Mocs1 A G 17: 49,740,303 (GRCm39) T77A probably damaging Het
Ndufs1 T C 1: 63,209,274 (GRCm39) N30D probably benign Het
Or1j11 T C 2: 36,312,126 (GRCm39) S239P probably damaging Het
Or4a71 T A 2: 89,358,494 (GRCm39) K87* probably null Het
Otog C A 7: 45,937,885 (GRCm39) P1865T possibly damaging Het
Pabpc1l T C 2: 163,873,140 (GRCm39) S137P probably damaging Het
Pilrb1 C A 5: 137,855,657 (GRCm39) W78L probably damaging Het
Plekha6 A G 1: 133,214,085 (GRCm39) Y832C possibly damaging Het
Ppan C A 9: 20,803,199 (GRCm39) Q424K probably benign Het
Ppp1r12a T A 10: 108,087,782 (GRCm39) N544K probably damaging Het
Pramel16 T C 4: 143,676,294 (GRCm39) E270G probably benign Het
Pstpip2 A G 18: 77,961,155 (GRCm39) D246G possibly damaging Het
Rasef G A 4: 73,662,356 (GRCm39) T198I probably damaging Het
Rbm12 T C 2: 155,938,463 (GRCm39) H603R probably benign Het
Rims1 T C 1: 22,482,490 (GRCm39) R179G probably damaging Het
Scel T C 14: 103,811,836 (GRCm39) L288P possibly damaging Het
Sel1l A T 12: 91,778,726 (GRCm39) D696E probably benign Het
Slc4a8 A G 15: 100,689,482 (GRCm39) K416R possibly damaging Het
Tmem132b A T 5: 125,700,115 (GRCm39) M218L probably benign Het
Tnrc6a T C 7: 122,791,881 (GRCm39) S1800P probably benign Het
Tpcn1 A C 5: 120,680,015 (GRCm39) L576R probably damaging Het
Vmn2r34 T G 7: 7,675,723 (GRCm39) Q555P possibly damaging Het
Vwa8 C T 14: 79,335,801 (GRCm39) T1419I probably benign Het
Xrn2 T C 2: 146,855,081 (GRCm39) Y14H probably benign Het
Zfp1007 A G 5: 109,823,708 (GRCm39) C581R probably damaging Het
Zfyve28 A T 5: 34,382,376 (GRCm39) D241E probably benign 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
R6401:Ldb3 UTSW 14 34,299,291 (GRCm39) missense probably benign 0.33
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
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'- TCACTAATCATGGCTCGTGC -3'
(R):5'- CCTCATCAGCACCCCTATTGAG -3'

Sequencing Primer
(F):5'- TGGCTCGTGCATCCCATACAATAG -3'
(R):5'- CCTATTGAGCATGCTCCAGTGTG -3'
Posted On 2022-02-07