Incidental Mutation 'IGL00090:Ly9'
ID1941
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Ly9
Ensembl Gene ENSMUSG00000004707
Gene Namelymphocyte antigen 9
SynonymsT100, CD229, Lgp100, SLAMF3
Accession Numbers
Is this an essential gene? Non essential (E-score: 0.000) question?
Stock #IGL00090
Quality Score
Status
Chromosome1
Chromosomal Location171588624-171607410 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to T at 171593451 bp
ZygosityHeterozygous
Amino Acid Change Isoleucine to Asparagine at position 624 (I624N)
Ref Sequence ENSEMBL: ENSMUSP00000106908 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000004827] [ENSMUST00000068878] [ENSMUST00000111277] [ENSMUST00000143463] [ENSMUST00000194797]
Predicted Effect probably damaging
Transcript: ENSMUST00000004827
AA Change: I514N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: I514N

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: I624N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: I624N

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: I624N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: I624N

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 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
Validation Efficiency
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: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4932415D10Rik T G 10: 82,283,752 M4475L probably benign Het
Abcb5 T C 12: 118,890,610 T857A probably benign Het
Abcc9 A T 6: 142,633,190 probably benign Het
Adam11 A G 11: 102,776,831 T709A probably benign Het
Adgre1 A G 17: 57,450,055 I771V probably benign Het
Adgrv1 T G 13: 81,405,408 probably null Het
Adgrv1 C T 13: 81,578,101 D602N probably damaging Het
Adra1d G T 2: 131,561,677 D164E possibly damaging Het
Ago3 A G 4: 126,371,541 L319P probably damaging Het
Aim2 A G 1: 173,455,465 S38G probably benign Het
Apoh A G 11: 108,395,834 D28G probably benign Het
Atm C T 9: 53,524,443 R189K probably damaging Het
Bbs1 T C 19: 4,893,010 T451A probably benign Het
BC034090 T C 1: 155,225,447 D719G possibly damaging Het
Bcr T C 10: 75,157,071 probably benign Het
Bmp2 A T 2: 133,561,027 Q166L probably benign Het
Bms1 A T 6: 118,404,583 S665T probably benign Het
Ccser1 A T 6: 62,380,142 T855S possibly damaging Het
Cfap36 C T 11: 29,222,875 V217M probably benign Het
Clca3b T C 3: 144,836,632 N470D probably damaging Het
Cort A G 4: 149,125,295 F100S probably damaging Het
Cyp4f14 G T 17: 32,914,566 D105E probably benign Het
Dnah1 A G 14: 31,287,873 S1913P probably benign Het
Fam91a1 A T 15: 58,430,735 H308L probably damaging Het
Fbn1 A C 2: 125,324,947 I2016M probably damaging Het
Fibcd1 T A 2: 31,833,874 Q251L possibly damaging Het
Flg2 T A 3: 93,202,109 Y481* probably null Het
Mapt C T 11: 104,322,485 S301L probably damaging Het
Meiob G A 17: 24,823,629 V144I probably benign Het
Muc4 G A 16: 32,754,086 G1321R probably benign Het
Myo5a T A 9: 75,161,497 C660* probably null Het
Necab3 G T 2: 154,547,568 probably benign Het
Nr2c2ap A G 8: 70,132,629 Y93C probably damaging Het
Nxpe5 A G 5: 138,248,834 D356G probably benign Het
Olfr1331 T A 4: 118,869,287 Y168N probably damaging Het
Olfr225 A T 11: 59,613,321 Y119F possibly damaging Het
Plce1 A G 19: 38,745,788 Q1544R probably damaging Het
Plppr4 T A 3: 117,322,220 T605S probably benign Het
Poglut1 C A 16: 38,542,916 W167L possibly damaging Het
Pou2f1 G T 1: 165,902,298 R162S probably damaging Het
Ptprf A G 4: 118,223,220 probably benign Het
Reln C A 5: 22,039,565 G805V possibly damaging Het
Rexo2 A G 9: 48,474,447 S126P probably damaging Het
Robo4 A G 9: 37,411,104 S844G probably damaging Het
Scn7a A G 2: 66,683,327 probably benign Het
Sdc1 A G 12: 8,790,459 T75A possibly damaging Het
Slc38a4 C T 15: 97,019,809 E12K probably benign Het
Tbck T C 3: 132,743,093 probably null Het
Tex2 A T 11: 106,568,535 V23E probably damaging Het
Zfp770 A G 2: 114,195,932 V552A probably benign Het
Zfyve26 T C 12: 79,249,460 probably benign Het
Other mutations in Ly9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00640:Ly9 APN 1 171601879 missense possibly damaging 0.65
IGL01899:Ly9 APN 1 171607247 missense probably damaging 0.99
IGL02714:Ly9 APN 1 171605118 missense possibly damaging 0.60
IGL03086:Ly9 APN 1 171605170 missense probably benign 0.01
R0647:Ly9 UTSW 1 171599808 missense probably damaging 1.00
R1292:Ly9 UTSW 1 171589103 unclassified probably null
R1422:Ly9 UTSW 1 171601212 missense probably damaging 1.00
R1598:Ly9 UTSW 1 171596507 missense probably benign 0.03
R1985:Ly9 UTSW 1 171599773 missense probably damaging 1.00
R2219:Ly9 UTSW 1 171597681 splice site probably null
R2427:Ly9 UTSW 1 171607232 missense probably damaging 0.99
R3764:Ly9 UTSW 1 171594144 missense possibly damaging 0.92
R3815:Ly9 UTSW 1 171589085 missense possibly damaging 0.95
R3816:Ly9 UTSW 1 171589085 missense possibly damaging 0.95
R3817:Ly9 UTSW 1 171589085 missense possibly damaging 0.95
R3819:Ly9 UTSW 1 171589085 missense possibly damaging 0.95
R4590:Ly9 UTSW 1 171593875 nonsense probably null
R4653:Ly9 UTSW 1 171594029 missense probably benign 0.41
R4755:Ly9 UTSW 1 171607238 missense probably damaging 0.99
R4871:Ly9 UTSW 1 171607330 intron probably benign
R5167:Ly9 UTSW 1 171605205 missense probably damaging 1.00
R5203:Ly9 UTSW 1 171599779 missense probably damaging 1.00
R5270:Ly9 UTSW 1 171601162 missense probably damaging 0.99
R5692:Ly9 UTSW 1 171605187 frame shift probably null
R5996:Ly9 UTSW 1 171601828 missense probably damaging 1.00
R6389:Ly9 UTSW 1 171596537 missense probably damaging 1.00
R6391:Ly9 UTSW 1 171601008 missense possibly damaging 0.76
R6457:Ly9 UTSW 1 171589095 missense probably damaging 1.00
R6730:Ly9 UTSW 1 171605169 missense probably benign 0.14
R6732:Ly9 UTSW 1 171594085 missense possibly damaging 0.74
R6862:Ly9 UTSW 1 171601155 missense probably benign 0.21
R6866:Ly9 UTSW 1 171605279 missense probably damaging 0.99
X0062:Ly9 UTSW 1 171605221 missense possibly damaging 0.82
Posted On2011-07-12