Incidental Mutation 'R5558:Lca5'
ID 436413
Institutional Source Beutler Lab
Gene Symbol Lca5
Ensembl Gene ENSMUSG00000032258
Gene Name Leber congenital amaurosis 5 (human)
Synonyms 4930431B11Rik, ORF64, 5730406O13Rik
MMRRC Submission 043115-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.454) question?
Stock # R5558 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 83272346-83323180 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 83283796 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 246 (S246T)
Ref Sequence ENSEMBL: ENSMUSP00000034791 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034791] [ENSMUST00000034793] [ENSMUST00000190514]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000034791
AA Change: S246T

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000034791
Gene: ENSMUSG00000032258
AA Change: S246T

DomainStartEndE-ValueType
low complexity region 25 40 N/A INTRINSIC
Pfam:Lebercilin 103 295 2.6e-66 PFAM
low complexity region 306 315 N/A INTRINSIC
low complexity region 617 627 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000034793
AA Change: S246T

PolyPhen 2 Score 0.477 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000034793
Gene: ENSMUSG00000032258
AA Change: S246T

DomainStartEndE-ValueType
low complexity region 25 40 N/A INTRINSIC
Pfam:Lebercilin 102 295 4.8e-71 PFAM
low complexity region 306 315 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000190514
AA Change: S246T

PolyPhen 2 Score 0.477 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000140753
Gene: ENSMUSG00000032258
AA Change: S246T

DomainStartEndE-ValueType
low complexity region 25 40 N/A INTRINSIC
Pfam:Lebercilin 102 295 5.8e-71 PFAM
low complexity region 306 315 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191225
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.2%
  • 20x: 94.6%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is thought to be involved in centrosomal or ciliary functions. Mutations in this gene cause Leber congenital amaurosis type V. Alternatively spliced transcript variants are described. [provided by RefSeq, Oct 2009]
PHENOTYPE: Mice homozygous for a gene trapped allele exhibit retinal patches of depigmentation, lack rod and cone ERG responses to light stimuli, and show loss of ciliary intraflagellar transport function in photoreceptors leading to failure of outer segment formation and photoreceptor degeneration. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcg4 T C 9: 44,192,705 (GRCm39) K177E probably damaging Het
Acvr1 T C 2: 58,349,029 (GRCm39) T378A probably damaging Het
Agtpbp1 A G 13: 59,630,394 (GRCm39) V779A probably benign Het
Alms1 C T 6: 85,618,311 (GRCm39) Q2786* probably null Het
Arhgef28 A C 13: 98,097,968 (GRCm39) L882R probably damaging Het
Cbx2 A G 11: 118,919,775 (GRCm39) T447A probably benign Het
Ch25h A G 19: 34,451,863 (GRCm39) W222R probably damaging Het
Chsy3 T G 18: 59,309,469 (GRCm39) S241A probably damaging Het
Cyfip1 T C 7: 55,541,749 (GRCm39) S345P possibly damaging Het
Cyp4a30b C A 4: 115,316,063 (GRCm39) D291E probably damaging Het
Dcstamp A G 15: 39,622,936 (GRCm39) Y419C probably damaging Het
Eif3d G A 15: 77,846,047 (GRCm39) R359C probably damaging Het
Elavl4 C A 4: 110,063,800 (GRCm39) G267V probably benign Het
Gars1 T C 6: 55,042,592 (GRCm39) S442P probably damaging Het
Gas6 C T 8: 13,516,764 (GRCm39) R578Q probably null Het
H4c4 C A 13: 23,765,779 (GRCm39) N65K possibly damaging Het
Ifitm6 T C 7: 140,595,985 (GRCm39) I103V probably benign Het
Igsf5 T A 16: 96,187,731 (GRCm39) I241N possibly damaging Het
Iqce A G 5: 140,657,560 (GRCm39) probably null Het
Khdc4 A C 3: 88,600,403 (GRCm39) H164P probably damaging Het
Kif20b C A 19: 34,928,949 (GRCm39) Q1192K probably damaging Het
Lap3 A G 5: 45,662,093 (GRCm39) N298D probably benign Het
Mrps5 G A 2: 127,444,355 (GRCm39) G330S probably damaging Het
Myh15 C T 16: 48,889,900 (GRCm39) R164C probably benign Het
Myo19 C G 11: 84,801,274 (GRCm39) P940R probably damaging Het
Or10j7 T C 1: 173,011,585 (GRCm39) R139G probably benign Het
Or5b12b T C 19: 12,861,751 (GRCm39) F169L probably benign Het
Pcdh10 A G 3: 45,338,603 (GRCm39) D920G probably damaging Het
Pgm5 A T 19: 24,801,815 (GRCm39) probably null Het
Phactr4 T C 4: 132,105,766 (GRCm39) E137G probably damaging Het
Pkn1 C T 8: 84,411,351 (GRCm39) V239M probably damaging Het
Plcz1 T A 6: 139,985,481 (GRCm39) D20V probably damaging Het
Prkca A T 11: 107,872,473 (GRCm39) I429N probably damaging Het
Ptk2 A T 15: 73,176,294 (GRCm39) Y251N probably damaging Het
R3hdm2 T C 10: 127,280,271 (GRCm39) F31S probably damaging Het
Rab11fip1 T A 8: 27,642,003 (GRCm39) E932V probably damaging Het
Rilp A G 11: 75,402,251 (GRCm39) Y250C probably damaging Het
Sclt1 A G 3: 41,616,025 (GRCm39) I474T probably benign Het
Slc14a2 T A 18: 78,202,381 (GRCm39) D583V possibly damaging Het
Slc30a4 A G 2: 122,528,903 (GRCm39) I324T probably damaging Het
Slc6a5 G A 7: 49,577,321 (GRCm39) V326I probably benign Het
Slco1c1 C T 6: 141,513,222 (GRCm39) T617I probably damaging Het
Sntg1 A G 1: 8,484,495 (GRCm39) S442P possibly damaging Het
Sys1 G T 2: 164,306,429 (GRCm39) A128S possibly damaging Het
Tbc1d2 C T 4: 46,629,912 (GRCm39) G252R probably benign Het
Tmed5 A G 5: 108,272,462 (GRCm39) I212T probably benign Het
Tnks T C 8: 35,432,819 (GRCm39) M1V probably null Het
Trpa1 T C 1: 14,968,492 (GRCm39) H452R probably damaging Het
Trpm3 T C 19: 22,955,937 (GRCm39) V1133A probably damaging Het
Ttn T A 2: 76,555,395 (GRCm39) I30537F probably damaging Het
Ush2a T C 1: 188,530,024 (GRCm39) V3271A possibly damaging Het
Utp20 C G 10: 88,587,329 (GRCm39) G2489R probably damaging Het
Vmn1r70 A T 7: 10,368,402 (GRCm39) S278C probably benign Het
Wdpcp G A 11: 21,661,732 (GRCm39) A335T probably benign Het
Zc3h18 G T 8: 123,113,659 (GRCm39) R217L probably damaging Het
Zfp384 ACAGCAGCAGCAGCAGCAGCAGC ACAGCAGCAGCAGCAGCAGC 6: 125,013,472 (GRCm39) probably benign Het
Zfp955b C T 17: 33,521,161 (GRCm39) T210I possibly damaging Het
Other mutations in Lca5
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01073:Lca5 APN 9 83,277,528 (GRCm39) missense probably damaging 0.98
IGL01349:Lca5 APN 9 83,308,670 (GRCm39) missense probably damaging 1.00
IGL01918:Lca5 APN 9 83,305,201 (GRCm39) missense probably damaging 1.00
IGL02035:Lca5 APN 9 83,305,365 (GRCm39) missense probably damaging 1.00
IGL02276:Lca5 APN 9 83,280,638 (GRCm39) missense possibly damaging 0.79
IGL02425:Lca5 APN 9 83,281,774 (GRCm39) missense probably damaging 1.00
IGL02481:Lca5 APN 9 83,305,170 (GRCm39) missense probably damaging 1.00
IGL02483:Lca5 APN 9 83,305,170 (GRCm39) missense probably damaging 1.00
R0465:Lca5 UTSW 9 83,277,920 (GRCm39) nonsense probably null
R0610:Lca5 UTSW 9 83,281,792 (GRCm39) missense probably benign 0.24
R0811:Lca5 UTSW 9 83,281,806 (GRCm39) missense possibly damaging 0.95
R0812:Lca5 UTSW 9 83,281,806 (GRCm39) missense possibly damaging 0.95
R0968:Lca5 UTSW 9 83,305,222 (GRCm39) missense probably benign 0.01
R1891:Lca5 UTSW 9 83,277,661 (GRCm39) missense probably damaging 1.00
R5223:Lca5 UTSW 9 83,280,666 (GRCm39) missense probably benign 0.00
R5235:Lca5 UTSW 9 83,305,107 (GRCm39) nonsense probably null
R5260:Lca5 UTSW 9 83,305,276 (GRCm39) missense probably damaging 0.98
R5531:Lca5 UTSW 9 83,280,648 (GRCm39) missense probably benign 0.00
R5688:Lca5 UTSW 9 83,280,619 (GRCm39) missense probably benign 0.01
R5886:Lca5 UTSW 9 83,281,734 (GRCm39) missense probably benign 0.31
R6426:Lca5 UTSW 9 83,277,707 (GRCm39) nonsense probably null
R7108:Lca5 UTSW 9 83,305,222 (GRCm39) missense probably benign 0.25
R7151:Lca5 UTSW 9 83,280,693 (GRCm39) missense probably benign 0.20
R7314:Lca5 UTSW 9 83,277,563 (GRCm39) missense possibly damaging 0.86
R7378:Lca5 UTSW 9 83,277,583 (GRCm39) missense probably benign 0.00
R7468:Lca5 UTSW 9 83,305,509 (GRCm39) missense probably damaging 0.99
R7686:Lca5 UTSW 9 83,277,292 (GRCm39) missense probably benign 0.00
R8874:Lca5 UTSW 9 83,277,503 (GRCm39) missense probably damaging 1.00
R8934:Lca5 UTSW 9 83,273,909 (GRCm39) utr 3 prime probably benign
R8987:Lca5 UTSW 9 83,283,796 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GGTTTAGATGGCGTGAGAAATC -3'
(R):5'- GGTGTGTAAGGACTGATTACCC -3'

Sequencing Primer
(F):5'- TGAGAAATCATGCCGCCGTC -3'
(R):5'- GTGTAAGGACTGATTACCCATCATC -3'
Posted On 2016-10-24