Incidental Mutation 'R5802:Lypd6'
ID 501562
Institutional Source Beutler Lab
Gene Symbol Lypd6
Ensembl Gene ENSMUSG00000050447
Gene Name LY6/PLAUR domain containing 6
Synonyms E130115E03Rik
MMRRC Submission 043391-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.515) question?
Stock # R5802 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 50066429-50193569 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) C to T at 50173601 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 40 (T40I)
Ref Sequence ENSEMBL: ENSMUSP00000116803 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000053208] [ENSMUST00000112712] [ENSMUST00000126337] [ENSMUST00000128451] [ENSMUST00000169232]
AlphaFold Q8BPP5
Predicted Effect probably benign
Transcript: ENSMUST00000053208
AA Change: T40I

PolyPhen 2 Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000061578
Gene: ENSMUSG00000050447
AA Change: T40I

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
LU 47 141 1.04e-1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112712
AA Change: T40I

PolyPhen 2 Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000108332
Gene: ENSMUSG00000050447
AA Change: T40I

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
LU 47 141 1.04e-1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000126337
AA Change: T40I

PolyPhen 2 Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000119755
Gene: ENSMUSG00000050447
AA Change: T40I

DomainStartEndE-ValueType
signal peptide 1 22 N/A INTRINSIC
Blast:LU 47 70 1e-10 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000128451
AA Change: T40I

PolyPhen 2 Score 0.252 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000116803
Gene: ENSMUSG00000050447
AA Change: T40I

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Blast:LU 47 123 4e-51 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000169232
AA Change: T40I

PolyPhen 2 Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000131002
Gene: ENSMUSG00000050447
AA Change: T40I

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
LU 47 141 1.04e-1 SMART
Meta Mutation Damage Score 0.1881 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.7%
Validation Efficiency 97% (63/65)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Members of the LY6 protein family (see SLURP1; MIM 606119), such as LYPD6, have at least one 80-amino acid LU domain that contains 10 conserved cysteines with a defined disulfide-bonding pattern (Zhang et al., 2010 [PubMed 19653121]).[supplied by OMIM, Apr 2010]
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A830018L16Rik A T 1: 11,950,964 D383V probably damaging Het
Abca4 A T 3: 122,054,232 L67F probably damaging Het
Abcc9 C A 6: 142,656,676 probably null Het
Atp2a3 T C 11: 72,972,882 V175A probably damaging Het
B3galt4 T A 17: 33,950,757 D169V probably damaging Het
Bsn C T 9: 108,113,009 R1848Q possibly damaging Het
Camkk2 T C 5: 122,734,244 E90G probably damaging Het
Cdon T A 9: 35,454,420 I155N probably damaging Het
Cep70 A G 9: 99,296,405 N519D probably damaging Het
Clgn T C 8: 83,425,614 S582P probably damaging Het
Cnga3 T C 1: 37,260,925 F280S probably damaging Het
Dennd4c C T 4: 86,811,453 T764M probably benign Het
Dis3 A T 14: 99,099,664 S4T probably damaging Het
Dlgap1 T C 17: 70,766,091 probably null Het
Dnah17 C T 11: 118,036,446 V3839I possibly damaging Het
Dnajc1 A G 2: 18,284,739 Y286H probably benign Het
Dynap T A 18: 70,241,002 D151V unknown Het
Ednrb A G 14: 103,821,714 F292S probably damaging Het
Eef1a1 A G 9: 78,479,036 S396P probably damaging Het
Fancg A G 4: 43,006,582 F324S probably benign Het
Fbxw11 T A 11: 32,711,790 S56T probably benign Het
Gm13178 T A 4: 144,703,636 D261V probably damaging Het
Gm14409 T C 2: 177,265,256 T150A possibly damaging Het
Gm17535 G C 9: 3,035,758 V209L probably benign Homo
Gm20767 G A 13: 120,154,913 S96N possibly damaging Het
Gm5592 C T 7: 41,219,105 probably benign Het
Gm7030 A G 17: 36,111,287 probably benign Het
Gpr137 C T 19: 6,942,005 W51* probably null Het
Hbb-bs T C 7: 103,826,672 Y146C probably damaging Het
Herc1 G T 9: 66,462,878 C2982F probably damaging Het
Hnrnpa3 T A 2: 75,665,056 N309K unknown Het
Hydin A T 8: 110,452,060 I1096F possibly damaging Het
Klf12 A G 14: 100,022,894 V133A probably benign Het
Lats2 A T 14: 57,694,418 Y848N probably damaging Het
Loxl3 A G 6: 83,049,289 T453A possibly damaging Het
Ltn1 T G 16: 87,415,681 H664P probably benign Het
Nbeal1 A T 1: 60,272,221 T1817S probably benign Het
Nub1 A C 5: 24,702,441 Y350S possibly damaging Het
Pbp2 A G 6: 135,309,876 Y158H possibly damaging Het
Ptpru C T 4: 131,788,377 E827K possibly damaging Het
Rap1a A G 3: 105,745,936 Y32H probably damaging Het
Raph1 T C 1: 60,488,673 N1143S possibly damaging Het
Rbl1 T C 2: 157,161,433 T859A probably benign Het
Rom1 A G 19: 8,928,824 L117P probably damaging Het
Senp6 T C 9: 80,118,644 probably benign Het
Sirpb1c T C 3: 15,832,076 M379V probably benign Het
Slc6a4 C T 11: 77,019,236 T439M probably damaging Het
Srsf12 G T 4: 33,230,929 R141L probably damaging Het
Stk10 C T 11: 32,596,748 P335L probably benign Het
Tecpr1 A T 5: 144,206,546 N670K probably benign Het
Tgds T C 14: 118,132,707 E8G probably benign Het
Tmem129 A G 5: 33,657,716 S38P probably damaging Het
Trappc9 T C 15: 72,685,339 E812G probably damaging Het
Trmt10b T A 4: 45,314,236 probably benign Het
Wapl A G 14: 34,692,320 T380A probably damaging Het
Xylt1 A T 7: 117,656,691 T829S probably benign Het
Zc3h6 C T 2: 129,015,559 P666L possibly damaging Het
Zfp703 C T 8: 26,979,205 P299L probably damaging Het
Other mutations in Lypd6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01470:Lypd6 APN 2 50188783 missense probably benign 0.16
IGL02476:Lypd6 APN 2 50190728 missense possibly damaging 0.84
R0098:Lypd6 UTSW 2 50190780 missense probably benign 0.01
R0098:Lypd6 UTSW 2 50190780 missense probably benign 0.01
R0302:Lypd6 UTSW 2 50165667 splice site probably benign
R0464:Lypd6 UTSW 2 50190678 missense probably damaging 1.00
R1577:Lypd6 UTSW 2 50190698 nonsense probably null
R1843:Lypd6 UTSW 2 50188762 missense possibly damaging 0.94
R2849:Lypd6 UTSW 2 50165652 missense probably damaging 1.00
R4663:Lypd6 UTSW 2 50173611 nonsense probably null
R4716:Lypd6 UTSW 2 50188843 critical splice donor site probably null
R8171:Lypd6 UTSW 2 50190747 missense possibly damaging 0.90
R8798:Lypd6 UTSW 2 50188762 missense possibly damaging 0.94
R9653:Lypd6 UTSW 2 50190746 missense probably benign 0.01
Z1177:Lypd6 UTSW 2 50190807 frame shift probably null
Predicted Primers PCR Primer
(F):5'- TCTAATCAGGAGTGGGCAGC -3'
(R):5'- ATGTACCAGGTCTTCAGGGC -3'

Sequencing Primer
(F):5'- GTGGGCAGCTTGTTCAAATACAAC -3'
(R):5'- CTGCGGACTCTCAAGCAG -3'
Posted On 2017-12-01