Incidental Mutation 'R6389:Ly9'
ID 515664
Institutional Source Beutler Lab
Gene Symbol Ly9
Ensembl Gene ENSMUSG00000004707
Gene Name lymphocyte antigen 9
Synonyms T100, Lgp100, CD229, SLAMF3
MMRRC Submission 044538-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6389 (G1)
Quality Score 225.009
Status Validated
Chromosome 1
Chromosomal Location 171416172-171434917 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to C at 171424105 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Cysteine at position 482 (S482C)
Ref Sequence ENSEMBL: ENSMUSP00000106908 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000004827] [ENSMUST00000068878] [ENSMUST00000111277] [ENSMUST00000143463] [ENSMUST00000194797]
AlphaFold Q01965
Predicted Effect probably damaging
Transcript: ENSMUST00000004827
AA Change: S372C

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: S372C

DomainStartEndE-ValueType
Pfam:Ig_3 46 116 7.9e-9 PFAM
Pfam:Ig_2 46 129 5.4e-10 PFAM
IG 143 246 1.49e-2 SMART
Pfam:Ig_3 251 320 4.1e-13 PFAM
Pfam:Ig_2 251 330 7.5e-6 PFAM
transmembrane domain 345 364 N/A INTRINSIC
low complexity region 420 436 N/A INTRINSIC
low complexity region 519 530 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000068878
AA Change: S482C

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: S482C

DomainStartEndE-ValueType
IG 52 151 8.72e-4 SMART
Pfam:Ig_3 156 226 5.6e-8 PFAM
Pfam:Ig_2 156 239 4e-8 PFAM
IG 253 356 1.49e-2 SMART
Pfam:Ig_3 361 430 5.4e-10 PFAM
low complexity region 433 441 N/A INTRINSIC
transmembrane domain 455 474 N/A INTRINSIC
low complexity region 530 546 N/A INTRINSIC
low complexity region 629 640 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000111277
AA Change: S482C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: S482C

DomainStartEndE-ValueType
IG 52 151 8.72e-4 SMART
Pfam:Ig_3 156 226 9.9e-9 PFAM
Pfam:Ig_2 156 239 6.8e-10 PFAM
IG 253 356 1.49e-2 SMART
Pfam:Ig_3 361 430 5e-13 PFAM
Pfam:Ig_2 361 440 9.4e-6 PFAM
transmembrane domain 455 474 N/A INTRINSIC
low complexity region 530 546 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000143463
SMART Domains Protein: ENSMUSP00000137924
Gene: ENSMUSG00000004707

DomainStartEndE-ValueType
transmembrane domain 28 50 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146596
Predicted Effect probably benign
Transcript: ENSMUST00000194797
SMART Domains Protein: ENSMUSP00000141898
Gene: ENSMUSG00000004709

DomainStartEndE-ValueType
IG 26 128 4.23e-2 SMART
Pfam:Ig_2 134 221 6.5e-5 PFAM
transmembrane domain 226 248 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.2%
  • 20x: 96.9%
Validation Efficiency 100% (57/57)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] LY9 belongs to the SLAM family of immunomodulatory receptors (see SLAMF1; MIM 603492) and interacts with the adaptor molecule SAP (SH2D1A; MIM 300490) (Graham et al., 2006 [PubMed 16365421]).[supplied by OMIM, Mar 2008]
PHENOTYPE: This locus controls an antigen on thymocytes, lymphocytes and bone marrow cells. The a allele determines Ly9.1 antigen in A/J, 129/Re, BALB/c and C3H/He; the b allele determines antigen Ly9.2 in the C57 family of strains, HTI/Go, MA/My, F/St and C58/Lw. Null mutants are viable, healthy and fertile. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4931406B18Rik A C 7: 43,147,254 (GRCm39) L326R possibly damaging Het
Abcb11 A T 2: 69,154,238 (GRCm39) N109K probably damaging Het
Actn1 T A 12: 80,221,296 (GRCm39) M586L probably benign Het
Ago4 T A 4: 126,401,037 (GRCm39) I603F probably damaging Het
Bicc1 A T 10: 70,794,752 (GRCm39) V135D probably damaging Het
Bms1 T C 6: 118,380,196 (GRCm39) N704D possibly damaging Het
Cadm4 A C 7: 24,198,959 (GRCm39) Q78P probably benign Het
Cfap74 T C 4: 155,507,793 (GRCm39) I248T possibly damaging Het
Clu G C 14: 66,208,771 (GRCm39) probably benign Het
Cnnm3 T C 1: 36,559,603 (GRCm39) V514A probably damaging Het
Cntd1 A T 11: 101,176,577 (GRCm39) I225F probably damaging Het
Col20a1 T C 2: 180,634,376 (GRCm39) probably null Het
Ctnnal1 A G 4: 56,813,849 (GRCm39) V640A probably benign Het
Cul4a A G 8: 13,190,278 (GRCm39) T572A probably benign Het
D16Ertd472e A G 16: 78,342,071 (GRCm39) S270P probably damaging Het
Dmp1 A T 5: 104,360,788 (GRCm39) N488I probably damaging Het
Dnah14 G A 1: 181,478,767 (GRCm39) probably null Het
Dst T C 1: 34,232,265 (GRCm39) L3464P probably damaging Het
Fnbp4 C T 2: 90,575,879 (GRCm39) P27S unknown Het
Fpr-rs3 A T 17: 20,844,230 (GRCm39) F304I probably damaging Het
Gm13941 T C 2: 110,928,734 (GRCm39) Q108R unknown Het
Hcn3 C T 3: 89,058,240 (GRCm39) A339T possibly damaging Het
Inpp5f A G 7: 128,279,780 (GRCm39) D460G probably damaging Het
Ism2 T C 12: 87,329,145 (GRCm39) E253G possibly damaging Het
Klrg1 T C 6: 122,248,431 (GRCm39) N156S probably damaging Het
Ksr2 A G 5: 117,552,907 (GRCm39) N5S probably benign Het
Lrrc7 T G 3: 157,891,063 (GRCm39) E368A probably damaging Het
Map3k1 T C 13: 111,905,975 (GRCm39) D289G probably damaging Het
Mcub T C 3: 129,712,357 (GRCm39) T173A probably benign Het
Mup16 T C 4: 61,437,177 (GRCm39) E48G probably damaging Het
Naf1 C T 8: 67,313,680 (GRCm39) S24L possibly damaging Het
Ncoa6 A G 2: 155,237,736 (GRCm39) S2024P probably damaging Het
Nop56 C A 2: 130,119,807 (GRCm39) Q83K probably damaging Het
Nt5e T C 9: 88,245,524 (GRCm39) Y265H probably damaging Het
Odad1 G T 7: 45,597,940 (GRCm39) V617F probably benign Het
Or4a27 A G 2: 88,559,016 (GRCm39) V309A probably benign Het
Or52p2 A T 7: 102,237,679 (GRCm39) N90K probably benign Het
Or5w8 C T 2: 87,688,367 (GRCm39) P283S probably damaging Het
Oxct2a T A 4: 123,217,220 (GRCm39) K54* probably null Het
Oxct2b G T 4: 123,010,367 (GRCm39) D96Y probably benign Het
Pisd A G 5: 32,922,191 (GRCm39) Y250H probably damaging Het
Plekhm1 G T 11: 103,257,720 (GRCm39) N1071K probably benign Het
Prr11 G A 11: 86,989,564 (GRCm39) T269I possibly damaging Het
Ptpn4 T A 1: 119,649,684 (GRCm39) H304L probably damaging Het
Rrp1b A G 17: 32,275,601 (GRCm39) K383E possibly damaging Het
Sel1l2 C A 2: 140,087,274 (GRCm39) A466S probably damaging Het
Slc9a4 A G 1: 40,619,844 (GRCm39) I57V probably benign Het
Spag9 A G 11: 93,977,137 (GRCm39) E81G probably damaging Het
Tbr1 A G 2: 61,636,631 (GRCm39) probably benign Het
Tnrc6c A G 11: 117,613,567 (GRCm39) D735G probably damaging Het
Tspan17 A T 13: 54,943,429 (GRCm39) probably null Het
Tyw5 T C 1: 57,430,658 (GRCm39) K175R probably damaging Het
Ube2o A C 11: 116,439,684 (GRCm39) I162R probably null Het
Ubr1 G T 2: 120,711,520 (GRCm39) T1458K probably benign Het
Vmn2r16 A T 5: 109,478,344 (GRCm39) Q33L probably benign Het
Zfp1007 G A 5: 109,823,885 (GRCm39) P522S possibly damaging Het
Zfp799 A G 17: 33,039,552 (GRCm39) L238P probably damaging Het
Other mutations in Ly9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00090:Ly9 APN 1 171,421,019 (GRCm39) missense probably damaging 1.00
IGL00640:Ly9 APN 1 171,429,447 (GRCm39) missense possibly damaging 0.65
IGL01899:Ly9 APN 1 171,434,815 (GRCm39) missense probably damaging 0.99
IGL02714:Ly9 APN 1 171,432,686 (GRCm39) missense possibly damaging 0.60
IGL03086:Ly9 APN 1 171,432,738 (GRCm39) missense probably benign 0.01
R0647:Ly9 UTSW 1 171,427,376 (GRCm39) missense probably damaging 1.00
R1292:Ly9 UTSW 1 171,416,671 (GRCm39) splice site probably null
R1422:Ly9 UTSW 1 171,428,780 (GRCm39) missense probably damaging 1.00
R1598:Ly9 UTSW 1 171,424,075 (GRCm39) missense probably benign 0.03
R1985:Ly9 UTSW 1 171,427,341 (GRCm39) missense probably damaging 1.00
R2219:Ly9 UTSW 1 171,425,249 (GRCm39) splice site probably null
R2427:Ly9 UTSW 1 171,434,800 (GRCm39) missense probably damaging 0.99
R3764:Ly9 UTSW 1 171,421,712 (GRCm39) missense possibly damaging 0.92
R3815:Ly9 UTSW 1 171,416,653 (GRCm39) missense possibly damaging 0.95
R3816:Ly9 UTSW 1 171,416,653 (GRCm39) missense possibly damaging 0.95
R3817:Ly9 UTSW 1 171,416,653 (GRCm39) missense possibly damaging 0.95
R3819:Ly9 UTSW 1 171,416,653 (GRCm39) missense possibly damaging 0.95
R4590:Ly9 UTSW 1 171,421,443 (GRCm39) nonsense probably null
R4653:Ly9 UTSW 1 171,421,597 (GRCm39) missense probably benign 0.41
R4755:Ly9 UTSW 1 171,434,806 (GRCm39) missense probably damaging 0.99
R4871:Ly9 UTSW 1 171,434,898 (GRCm39) intron probably benign
R5167:Ly9 UTSW 1 171,432,773 (GRCm39) missense probably damaging 1.00
R5203:Ly9 UTSW 1 171,427,347 (GRCm39) missense probably damaging 1.00
R5270:Ly9 UTSW 1 171,428,730 (GRCm39) missense probably damaging 0.99
R5692:Ly9 UTSW 1 171,432,755 (GRCm39) frame shift probably null
R5996:Ly9 UTSW 1 171,429,396 (GRCm39) missense probably damaging 1.00
R6391:Ly9 UTSW 1 171,428,576 (GRCm39) missense possibly damaging 0.76
R6457:Ly9 UTSW 1 171,416,663 (GRCm39) missense probably damaging 1.00
R6730:Ly9 UTSW 1 171,432,737 (GRCm39) missense probably benign 0.14
R6732:Ly9 UTSW 1 171,421,653 (GRCm39) missense possibly damaging 0.74
R6862:Ly9 UTSW 1 171,428,723 (GRCm39) missense probably benign 0.21
R6866:Ly9 UTSW 1 171,432,847 (GRCm39) missense probably damaging 0.99
R7455:Ly9 UTSW 1 171,421,507 (GRCm39) nonsense probably null
R8105:Ly9 UTSW 1 171,432,890 (GRCm39) splice site probably null
R8349:Ly9 UTSW 1 171,421,586 (GRCm39) missense probably damaging 0.99
R8449:Ly9 UTSW 1 171,421,586 (GRCm39) missense probably damaging 0.99
R8836:Ly9 UTSW 1 171,432,559 (GRCm39) nonsense probably null
R8838:Ly9 UTSW 1 171,421,569 (GRCm39) missense probably damaging 1.00
R8856:Ly9 UTSW 1 171,432,587 (GRCm39) missense probably benign 0.03
R8892:Ly9 UTSW 1 171,421,465 (GRCm39) missense possibly damaging 0.81
R9414:Ly9 UTSW 1 171,427,275 (GRCm39) missense probably damaging 0.99
R9713:Ly9 UTSW 1 171,428,756 (GRCm39) missense probably damaging 1.00
R9748:Ly9 UTSW 1 171,428,722 (GRCm39) missense possibly damaging 0.65
X0062:Ly9 UTSW 1 171,432,789 (GRCm39) missense possibly damaging 0.82
Z1176:Ly9 UTSW 1 171,421,628 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CAAACTACTTTCTTCCAGCATACTG -3'
(R):5'- TGGGCTCTGGATACTGCTTC -3'

Sequencing Primer
(F):5'- CAGGTATGTGGGTCCCCTAAATAC -3'
(R):5'- GGATACTGCTTCCCTTGGC -3'
Posted On 2018-05-04