Incidental Mutation 'R9101:Ly6a'
ID 691710
Institutional Source Beutler Lab
Gene Symbol Ly6a
Ensembl Gene ENSMUSG00000075602
Gene Name lymphocyte antigen 6 family member A
Synonyms Ly-6A.2, TAP, Ly-6E.1, Ly-6A/E, Sca1, Sca-1
MMRRC Submission 068915-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.076) question?
Stock # R9101 (G1)
Quality Score 225.009
Status Validated
Chromosome 15
Chromosomal Location 74866726-74869880 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 74869419 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 12 (L12Q)
Ref Sequence ENSEMBL: ENSMUSP00000023248 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023248] [ENSMUST00000186526] [ENSMUST00000187171] [ENSMUST00000187994] [ENSMUST00000189068] [ENSMUST00000190188]
AlphaFold P05533
Predicted Effect probably null
Transcript: ENSMUST00000023248
AA Change: L12Q

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000023248
Gene: ENSMUSG00000075602
AA Change: L12Q

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
LU 27 118 3.59e-39 SMART
low complexity region 121 134 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000186526
AA Change: L12Q

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000140998
Gene: ENSMUSG00000075602
AA Change: L12Q

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
LU 27 118 3.59e-39 SMART
low complexity region 121 134 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000187171
AA Change: L12Q

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000140099
Gene: ENSMUSG00000075602
AA Change: L12Q

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
LU 27 118 3.59e-39 SMART
low complexity region 121 134 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000187994
AA Change: L12Q

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000140287
Gene: ENSMUSG00000075602
AA Change: L12Q

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
LU 27 118 3.59e-39 SMART
low complexity region 121 134 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000189068
AA Change: L12Q

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000140638
Gene: ENSMUSG00000075602
AA Change: L12Q

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
LU 27 118 3.59e-39 SMART
low complexity region 121 134 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000190188
AA Change: L12Q

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.2%
Validation Efficiency 98% (59/60)
MGI Phenotype PHENOTYPE: Nullizygous mice show strain-dependent prenatal lethality, altered proliferative response by T lymphocytes, hematopoietic stem cell and progenitor defects, and age-related osteoporosis. Heterozygotes for a knock-in allele develop a myeloproliferative disorder and skin pathology at high penetrance. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam6b T C 12: 113,455,376 (GRCm39) V731A probably benign Het
Adamts7 T C 9: 90,071,794 (GRCm39) probably null Het
Afdn T C 17: 14,043,706 (GRCm39) V388A probably damaging Het
Alg3 A G 16: 20,427,599 (GRCm39) Y113H possibly damaging Het
Aox1 C T 1: 58,371,796 (GRCm39) P820L probably benign Het
Avil A G 10: 126,852,873 (GRCm39) D731G probably benign Het
Blvra C T 2: 126,927,890 (GRCm39) L47F probably damaging Het
Bmerb1 T A 16: 13,867,259 (GRCm39) I39N probably damaging Het
Ccdc85c C A 12: 108,240,917 (GRCm39) R159L unknown Het
Clcn2 T C 16: 20,525,979 (GRCm39) D797G probably benign Het
Cmklr1 G C 5: 113,752,043 (GRCm39) H319Q probably benign Het
Dclre1a A T 19: 56,532,738 (GRCm39) F619I possibly damaging Het
Dnajb1 C A 8: 84,335,119 (GRCm39) D53E probably benign Het
Dnmt1 T C 9: 20,852,839 (GRCm39) D89G probably damaging Het
Gck A G 11: 5,856,516 (GRCm39) Y214H probably damaging Het
Gm9507 A G 10: 77,647,650 (GRCm39) S10P unknown Het
Hacd2 G A 16: 34,920,156 (GRCm39) V138I probably benign Het
Hhip A T 8: 80,770,591 (GRCm39) V272D probably damaging Het
Hoga1 A C 19: 42,048,347 (GRCm39) T72P possibly damaging Het
Idh2 TCCCAGG T 7: 79,748,079 (GRCm39) probably benign Het
Kif21b G A 1: 136,078,893 (GRCm39) G414S probably damaging Het
Klk1b5 T A 7: 43,500,205 (GRCm39) D264E probably benign Het
Lars1 G A 18: 42,376,942 (GRCm39) R205C probably damaging Het
Mastl A G 2: 23,008,449 (GRCm39) *866Q probably null Het
Mpzl3 T A 9: 44,981,983 (GRCm39) M217K possibly damaging Het
Mroh2b T A 15: 4,929,935 (GRCm39) M7K probably benign Het
Mtarc2 T A 1: 184,554,687 (GRCm39) R273W probably null Het
Nefh A G 11: 4,890,925 (GRCm39) S565P probably damaging Het
Nox4 G A 7: 87,025,448 (GRCm39) R525Q probably benign Het
Nsd1 C T 13: 55,461,359 (GRCm39) L2632F Het
Or10d1 T A 9: 39,483,805 (GRCm39) Y250F probably benign Het
Or1a1b C T 11: 74,097,322 (GRCm39) C240Y probably damaging Het
Or4a71 A T 2: 89,358,721 (GRCm39) I11N possibly damaging Het
Or51ac3 A T 7: 103,213,680 (GRCm39) F269I possibly damaging Het
Or51r1 T C 7: 102,228,137 (GRCm39) V145A probably benign Het
Or5m10b A G 2: 85,694,523 (GRCm39) probably benign Het
Or5w18 T C 2: 87,632,924 (GRCm39) Y60H probably damaging Het
Pcdhga6 T C 18: 37,841,393 (GRCm39) V371A possibly damaging Het
Pdss2 A G 10: 43,269,945 (GRCm39) K263E possibly damaging Het
Phf3 C T 1: 30,843,026 (GRCm39) A1978T possibly damaging Het
Phykpl C A 11: 51,483,741 (GRCm39) T207K probably benign Het
Pkd2 T A 5: 104,628,230 (GRCm39) C435S probably damaging Het
Pramel11 T A 4: 143,623,646 (GRCm39) N176I probably benign Het
Pramel52-ps G A 5: 94,531,899 (GRCm39) C261Y probably damaging Het
Prkra T A 2: 76,478,184 (GRCm39) H6L probably benign Het
Prpf39 A G 12: 65,090,078 (GRCm39) K131E probably damaging Het
Prpf40a A G 2: 53,035,255 (GRCm39) V762A probably benign Het
Prr27 C T 5: 87,991,330 (GRCm39) T314I probably damaging Het
Ptges3 A G 10: 127,907,998 (GRCm39) D116G possibly damaging Het
Rab11fip5 G T 6: 85,317,675 (GRCm39) F1071L probably benign Het
Rsf1 GCG GCGACGGCGCCG 7: 97,229,114 (GRCm39) probably benign Het
Slc45a3 T C 1: 131,905,175 (GRCm39) V66A possibly damaging Het
Spata31e5 T A 1: 28,815,740 (GRCm39) D764V probably benign Het
Ten1 A G 11: 116,096,562 (GRCm39) Y72C probably damaging Het
Tenm3 A G 8: 48,745,186 (GRCm39) L1125S probably damaging Het
Thpo T A 16: 20,544,557 (GRCm39) I159F possibly damaging Het
Tmppe T C 9: 114,234,309 (GRCm39) S203P probably damaging Het
Ttc23l A T 15: 10,537,661 (GRCm39) I203N probably benign Het
Vars2 A G 17: 35,969,980 (GRCm39) L803P possibly damaging Het
Vmn2r110 T A 17: 20,794,471 (GRCm39) I733F Het
Xxylt1 T C 16: 30,899,745 (GRCm39) N137D possibly damaging Het
Zc3h13 G A 14: 75,561,042 (GRCm39) R544Q unknown Het
Zfhx4 C T 3: 5,477,198 (GRCm39) T3271I probably benign Het
Zfp943 T A 17: 22,212,392 (GRCm39) C493S possibly damaging Het
Other mutations in Ly6a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01607:Ly6a APN 15 74,867,262 (GRCm39) missense probably benign
R0281:Ly6a UTSW 15 74,867,236 (GRCm39) missense probably benign 0.28
R1224:Ly6a UTSW 15 74,868,327 (GRCm39) missense possibly damaging 0.64
R7201:Ly6a UTSW 15 74,868,325 (GRCm39) missense probably benign 0.01
R7774:Ly6a UTSW 15 74,869,416 (GRCm39) missense probably damaging 1.00
R8070:Ly6a UTSW 15 74,869,449 (GRCm39) missense probably damaging 1.00
R8176:Ly6a UTSW 15 74,868,300 (GRCm39) critical splice donor site probably null
R9095:Ly6a UTSW 15 74,867,333 (GRCm39) unclassified probably benign
Predicted Primers PCR Primer
(F):5'- CTGACAGGTTTACAGACCCAG -3'
(R):5'- TCCTCAGGGAAAGCTGTGTG -3'

Sequencing Primer
(F):5'- CTGACAGGTTTACAGACCCAGTAAAG -3'
(R):5'- AAAGCTGTGTGGAGGGTTGGAG -3'
Posted On 2021-12-30