Incidental Mutation 'R2002:Ly6c1'
ID 223256
Institutional Source Beutler Lab
Gene Symbol Ly6c1
Ensembl Gene ENSMUSG00000079018
Gene Name lymphocyte antigen 6 family member C1
Synonyms Ly6c, Ly-6C
MMRRC Submission 040012-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.062) question?
Stock # R2002 (G1)
Quality Score 225
Status Validated
Chromosome 15
Chromosomal Location 74915867-74920679 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 74920342 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Serine at position 7 (T7S)
Ref Sequence ENSEMBL: ENSMUSP00000139559 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000065408] [ENSMUST00000179762] [ENSMUST00000185200] [ENSMUST00000185372] [ENSMUST00000187347] [ENSMUST00000188845] [ENSMUST00000191216]
AlphaFold P0CW02
Predicted Effect probably benign
Transcript: ENSMUST00000065408
AA Change: T7S

PolyPhen 2 Score 0.162 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000066954
Gene: ENSMUSG00000079018
AA Change: T7S

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
LU 27 115 1.62e-32 SMART
low complexity region 117 131 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000179762
AA Change: T7S

PolyPhen 2 Score 0.162 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000137401
Gene: ENSMUSG00000079018
AA Change: T7S

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
LU 27 115 1.62e-32 SMART
low complexity region 117 131 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000185200
AA Change: T7S

PolyPhen 2 Score 0.292 (Sensitivity: 0.91; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000140622
Gene: ENSMUSG00000079018
AA Change: T7S

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
Pfam:UPAR_LY6 29 77 2.3e-8 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000185372
AA Change: T7S

PolyPhen 2 Score 0.292 (Sensitivity: 0.91; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000139948
Gene: ENSMUSG00000079018
AA Change: T7S

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
Pfam:UPAR_LY6 29 77 6.3e-6 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000187347
AA Change: T7S

PolyPhen 2 Score 0.162 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000139799
Gene: ENSMUSG00000079018
AA Change: T7S

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
LU 27 115 1.62e-32 SMART
low complexity region 117 131 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000188845
AA Change: T7S

PolyPhen 2 Score 0.624 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000139559
Gene: ENSMUSG00000079018
AA Change: T7S

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
LU 27 115 1.52e-28 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000191216
AA Change: T7S

PolyPhen 2 Score 0.063 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000140722
Gene: ENSMUSG00000079018
AA Change: T7S

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
LU 27 111 5.2e-27 SMART
Meta Mutation Damage Score 0.1795 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.2%
  • 20x: 91.6%
Validation Efficiency 97% (72/74)
Allele List at MGI
Other mutations in this stock
Total: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930548G14Rik T C 15: 46,489,002 (GRCm39) noncoding transcript Het
Abcb4 T A 5: 8,955,989 (GRCm39) S98T probably benign Het
Acan T C 7: 78,750,541 (GRCm39) S1771P probably damaging Het
Acvr1c T A 2: 58,205,987 (GRCm39) Q41L probably benign Het
Ak2 T A 4: 128,902,022 (GRCm39) S232T probably benign Het
Akr1e1 T A 13: 4,657,564 (GRCm39) probably benign Het
Ano7 T C 1: 93,328,303 (GRCm39) probably benign Het
Aox1 T A 1: 58,086,300 (GRCm39) H68Q possibly damaging Het
Apaf1 A G 10: 90,897,676 (GRCm39) V269A possibly damaging Het
Apba2 A T 7: 64,383,290 (GRCm39) I368F probably damaging Het
Armc3 A G 2: 19,293,747 (GRCm39) M513V probably benign Het
Asb5 G A 8: 55,036,655 (GRCm39) V116M probably damaging Het
Atg16l2 A G 7: 100,944,127 (GRCm39) S280P possibly damaging Het
Atp6v0c G T 17: 24,383,835 (GRCm39) T40K probably damaging Het
Cdk2ap2 A G 19: 4,147,903 (GRCm39) M57V possibly damaging Het
Cip2a T C 16: 48,826,214 (GRCm39) probably benign Het
Ctnnd1 T C 2: 84,450,704 (GRCm39) N172S probably benign Het
Ddx55 T A 5: 124,704,503 (GRCm39) V370E probably damaging Het
Ddx6 A G 9: 44,518,831 (GRCm39) T48A probably benign Het
Dnah10 C T 5: 124,911,052 (GRCm39) R4490W probably damaging Het
Dspp T A 5: 104,326,425 (GRCm39) S929R unknown Het
Erbb3 T C 10: 128,422,094 (GRCm39) Y50C probably benign Het
Fam209 C A 2: 172,314,689 (GRCm39) N59K probably benign Het
Fgd3 T C 13: 49,449,931 (GRCm39) E106G probably benign Het
Frmd4a A C 2: 4,577,176 (GRCm39) K344T probably damaging Het
Gbe1 A G 16: 70,325,814 (GRCm39) E617G probably damaging Het
Gm5089 T A 14: 122,673,686 (GRCm39) I12F unknown Het
Gm7052 T A 17: 22,258,920 (GRCm39) probably benign Het
Gria1 A T 11: 56,902,930 (GRCm39) N24I possibly damaging Het
Grin2b T C 6: 135,710,243 (GRCm39) E1101G probably damaging Het
Hjurp GT GTT 1: 88,194,246 (GRCm39) probably null Het
Kcnma1 A C 14: 23,387,097 (GRCm39) S982A probably damaging Het
Khdrbs3 T A 15: 68,885,328 (GRCm39) probably benign Het
Kif23 A T 9: 61,834,666 (GRCm39) C426* probably null Het
Lmo7 G T 14: 102,124,497 (GRCm39) A319S probably benign Het
Magel2 G A 7: 62,028,844 (GRCm39) V583I unknown Het
Mamdc4 A T 2: 25,457,244 (GRCm39) W548R probably damaging Het
Mfsd2a C T 4: 122,850,609 (GRCm39) R88Q probably damaging Het
Mkrn1 T C 6: 39,382,737 (GRCm39) T158A probably benign Het
Mroh2b G T 15: 4,955,166 (GRCm39) D720Y probably damaging Het
Mycbp2 A G 14: 103,485,839 (GRCm39) V1041A probably damaging Het
Ncam2 A T 16: 81,386,586 (GRCm39) H655L possibly damaging Het
Npas2 T C 1: 39,377,276 (GRCm39) V546A probably benign Het
Nrxn3 G A 12: 90,299,089 (GRCm39) A400T probably damaging Het
Oog3 G T 4: 143,884,675 (GRCm39) H420Q possibly damaging Het
Or3a10 A T 11: 73,935,865 (GRCm39) S78R possibly damaging Het
Or5ap2 T A 2: 85,680,744 (GRCm39) V316E probably benign Het
Or8k28 T C 2: 86,285,817 (GRCm39) H266R probably benign Het
Pak5 T A 2: 135,958,557 (GRCm39) H177L probably benign Het
Pcca A G 14: 123,124,477 (GRCm39) I683V probably benign Het
Pea15a T C 1: 172,026,252 (GRCm39) I90V probably benign Het
Plagl1 C A 10: 13,004,402 (GRCm39) probably benign Het
Prmt1 A G 7: 44,628,148 (GRCm39) V237A probably damaging Het
Ptprz1 T A 6: 23,027,833 (GRCm39) Y910* probably null Het
Rasal3 T A 17: 32,612,585 (GRCm39) T757S probably damaging Het
Rbbp8 T C 18: 11,860,223 (GRCm39) probably benign Het
S1pr1 A G 3: 115,506,544 (GRCm39) S17P probably benign Het
Scel G A 14: 103,779,421 (GRCm39) V131M probably damaging Het
Scn2a G A 2: 65,512,427 (GRCm39) R188Q probably null Het
Snap29 T A 16: 17,224,190 (GRCm39) Y68* probably null Het
Spdl1 T C 11: 34,713,473 (GRCm39) T199A probably benign Het
Srbd1 T C 17: 86,449,828 (GRCm39) N14D probably benign Het
Ston1 G A 17: 88,942,957 (GRCm39) G121D probably benign Het
Syt16 G A 12: 74,281,977 (GRCm39) G367E possibly damaging Het
Tdpoz1 T C 3: 93,578,710 (GRCm39) T25A possibly damaging Het
Tmem182 T A 1: 40,845,355 (GRCm39) Y77N probably damaging Het
Tmprss11f A T 5: 86,687,627 (GRCm39) probably benign Het
Trp73 T C 4: 154,165,902 (GRCm39) T56A probably damaging Het
Trpm3 A G 19: 22,959,947 (GRCm39) K1194R probably damaging Het
Ttc39c T A 18: 12,830,935 (GRCm39) probably null Het
Ube4b T C 4: 149,468,254 (GRCm39) D174G probably benign Het
Vmn1r211 A T 13: 23,035,953 (GRCm39) M238K probably damaging Het
Wsb2 T A 5: 117,508,798 (GRCm39) N77K probably benign Het
Xkr4 C T 1: 3,741,318 (GRCm39) R85Q probably benign Het
Zmynd11 T A 13: 9,739,514 (GRCm39) probably null Het
Other mutations in Ly6c1
AlleleSourceChrCoordTypePredicted EffectPPH Score
R3881:Ly6c1 UTSW 15 74,917,436 (GRCm39) missense probably benign 0.07
R5986:Ly6c1 UTSW 15 74,917,457 (GRCm39) missense probably damaging 1.00
R6462:Ly6c1 UTSW 15 74,916,178 (GRCm39) unclassified probably benign
R6966:Ly6c1 UTSW 15 74,917,289 (GRCm39) unclassified probably benign
R7169:Ly6c1 UTSW 15 74,916,495 (GRCm39) missense probably benign 0.00
R7355:Ly6c1 UTSW 15 74,919,256 (GRCm39) missense possibly damaging 0.78
R7583:Ly6c1 UTSW 15 74,920,346 (GRCm39) missense probably damaging 1.00
R9037:Ly6c1 UTSW 15 74,917,300 (GRCm39) missense probably damaging 1.00
R9038:Ly6c1 UTSW 15 74,917,300 (GRCm39) missense probably damaging 1.00
R9039:Ly6c1 UTSW 15 74,917,300 (GRCm39) missense probably damaging 1.00
R9224:Ly6c1 UTSW 15 74,916,465 (GRCm39) missense probably benign 0.00
R9354:Ly6c1 UTSW 15 74,916,471 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- TGGCAGGTTTACAGACCCAG -3'
(R):5'- AGGCAGACATGTATTCCTCAGG -3'

Sequencing Primer
(F):5'- ATCCCAGTACAGGAGGCTTC -3'
(R):5'- CCTCAGGGAAAGCTGTGTG -3'
Posted On 2014-08-25