Incidental Mutation 'R0647:Ly9'
| ID |
57238 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ly9
|
| Ensembl Gene |
ENSMUSG00000004707 |
| Gene Name |
lymphocyte antigen 9 |
| Synonyms |
T100, Lgp100, CD229, SLAMF3 |
| MMRRC Submission |
038832-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R0647 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
1 |
| Chromosomal Location |
171416172-171434917 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 171427376 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 393
(Y393C)
|
| 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: Y283C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: Y283C
| Domain | Start | End | E-Value | Type |
|---|
|
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: Y393C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: Y393C
| Domain | Start | End | E-Value | Type |
|---|
|
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: Y393C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: Y393C
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
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: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.1%
|
| 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: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamts2 |
C |
A |
11: 50,494,265 (GRCm39) |
T113K |
probably damaging |
Het |
| Adgre1 |
T |
A |
17: 57,718,003 (GRCm39) |
N338K |
probably damaging |
Het |
| Aggf1 |
A |
T |
13: 95,508,164 (GRCm39) |
|
probably null |
Het |
| Apc2 |
A |
T |
10: 80,140,762 (GRCm39) |
I206F |
probably damaging |
Het |
| Carmil3 |
T |
C |
14: 55,739,892 (GRCm39) |
|
probably null |
Het |
| Ccdc110 |
A |
C |
8: 46,396,425 (GRCm39) |
E772A |
probably damaging |
Het |
| Cdh23 |
A |
G |
10: 60,143,681 (GRCm39) |
F2977L |
probably damaging |
Het |
| Cdh23 |
A |
T |
10: 60,159,153 (GRCm39) |
Y2207* |
probably null |
Het |
| Cfap20dc |
T |
A |
14: 8,536,655 (GRCm38) |
D184V |
possibly damaging |
Het |
| Chd4 |
T |
A |
6: 125,086,086 (GRCm39) |
N908K |
probably damaging |
Het |
| Chst9 |
A |
G |
18: 15,585,726 (GRCm39) |
I279T |
probably damaging |
Het |
| Ctnna3 |
A |
T |
10: 63,656,203 (GRCm39) |
N261I |
probably benign |
Het |
| Dlgap2 |
A |
T |
8: 14,777,591 (GRCm39) |
S279C |
possibly damaging |
Het |
| Dock4 |
G |
A |
12: 40,760,883 (GRCm39) |
E524K |
probably damaging |
Het |
| Fabp12 |
T |
A |
3: 10,311,096 (GRCm39) |
N122I |
possibly damaging |
Het |
| Fam184b |
T |
C |
5: 45,741,932 (GRCm39) |
T100A |
probably benign |
Het |
| Fbxl5 |
T |
C |
5: 43,925,411 (GRCm39) |
D176G |
probably damaging |
Het |
| Fcho1 |
C |
T |
8: 72,165,204 (GRCm39) |
A418T |
probably benign |
Het |
| Foxe1 |
A |
G |
4: 46,344,477 (GRCm39) |
N95S |
possibly damaging |
Het |
| Frem3 |
A |
G |
8: 81,341,814 (GRCm39) |
E1369G |
probably damaging |
Het |
| Frmpd4 |
C |
T |
X: 166,272,006 (GRCm39) |
E483K |
probably damaging |
Het |
| Gbp11 |
T |
C |
5: 105,478,830 (GRCm39) |
K203E |
possibly damaging |
Het |
| Hs3st6 |
C |
T |
17: 24,977,134 (GRCm39) |
R205C |
probably damaging |
Het |
| Ifitm10 |
C |
T |
7: 141,909,772 (GRCm39) |
S179N |
probably damaging |
Het |
| Irx2 |
A |
C |
13: 72,778,799 (GRCm39) |
N121T |
probably damaging |
Het |
| Itih1 |
A |
T |
14: 30,657,820 (GRCm39) |
V417E |
probably damaging |
Het |
| Itpr1 |
A |
C |
6: 108,360,659 (GRCm39) |
E695A |
probably damaging |
Het |
| Kif1c |
T |
A |
11: 70,616,967 (GRCm39) |
I755K |
probably damaging |
Het |
| Lamb3 |
A |
G |
1: 193,013,104 (GRCm39) |
E443G |
probably damaging |
Het |
| Lrp1 |
G |
C |
10: 127,407,346 (GRCm39) |
T1865R |
probably damaging |
Het |
| Lrrc8b |
T |
A |
5: 105,628,473 (GRCm39) |
I273K |
possibly damaging |
Het |
| Mphosph8 |
T |
C |
14: 56,911,862 (GRCm39) |
V295A |
probably benign |
Het |
| Nlrp5 |
T |
A |
7: 23,117,132 (GRCm39) |
D269E |
probably damaging |
Het |
| Or1r1 |
G |
A |
11: 73,874,597 (GRCm39) |
A279V |
probably damaging |
Het |
| Or2t6 |
T |
G |
14: 14,175,858 (GRCm38) |
T75P |
probably benign |
Het |
| Or4k44 |
A |
G |
2: 111,367,704 (GRCm39) |
V310A |
probably benign |
Het |
| Or52u1 |
T |
G |
7: 104,237,322 (GRCm39) |
F104V |
probably damaging |
Het |
| Or5p50 |
T |
A |
7: 107,422,218 (GRCm39) |
I153F |
probably benign |
Het |
| Otud3 |
A |
G |
4: 138,640,948 (GRCm39) |
L64P |
probably damaging |
Het |
| Pcdh17 |
A |
T |
14: 84,685,213 (GRCm39) |
H560L |
possibly damaging |
Het |
| Pcdhb21 |
T |
C |
18: 37,646,913 (GRCm39) |
V14A |
probably damaging |
Het |
| Prss3l |
A |
T |
6: 41,420,275 (GRCm39) |
F150L |
probably benign |
Het |
| Rbfox1 |
A |
T |
16: 7,042,248 (GRCm39) |
Q14L |
probably damaging |
Het |
| Rbm44 |
A |
G |
1: 91,084,650 (GRCm39) |
D665G |
probably benign |
Het |
| Rc3h2 |
C |
T |
2: 37,299,542 (GRCm39) |
V163M |
probably damaging |
Het |
| Sash1 |
T |
A |
10: 8,605,316 (GRCm39) |
R1025W |
probably damaging |
Het |
| Sgpl1 |
A |
G |
10: 60,949,267 (GRCm39) |
S146P |
probably damaging |
Het |
| Slc27a2 |
G |
A |
2: 126,429,836 (GRCm39) |
D615N |
probably benign |
Het |
| Smap1 |
A |
G |
1: 23,892,559 (GRCm39) |
I135T |
probably damaging |
Het |
| Snapc3 |
A |
G |
4: 83,368,466 (GRCm39) |
D321G |
probably damaging |
Het |
| St6galnac4 |
C |
T |
2: 32,479,460 (GRCm39) |
R6C |
probably damaging |
Het |
| Syne2 |
C |
T |
12: 75,934,977 (GRCm39) |
P153L |
probably benign |
Het |
| Tiprl |
A |
G |
1: 165,050,092 (GRCm39) |
|
probably null |
Het |
| Tmem94 |
A |
G |
11: 115,687,621 (GRCm39) |
N1160S |
probably damaging |
Het |
| Trim65 |
G |
A |
11: 116,019,036 (GRCm39) |
R168C |
possibly damaging |
Het |
| Txndc16 |
A |
T |
14: 45,406,732 (GRCm39) |
I241N |
probably damaging |
Het |
| Txndc16 |
T |
A |
14: 45,402,818 (GRCm39) |
R101* |
probably null |
Het |
| Ugt2b38 |
A |
G |
5: 87,571,328 (GRCm39) |
S235P |
probably benign |
Het |
| Ugt3a1 |
A |
T |
15: 9,310,635 (GRCm39) |
M306L |
probably benign |
Het |
| Vmn1r23 |
T |
A |
6: 57,903,169 (GRCm39) |
Y203F |
probably benign |
Het |
| Vmn2r3 |
T |
A |
3: 64,183,046 (GRCm39) |
I218F |
probably damaging |
Het |
| Wdfy4 |
A |
G |
14: 32,831,656 (GRCm39) |
C857R |
possibly damaging |
Het |
| Zfp493 |
A |
C |
13: 67,931,994 (GRCm39) |
K31T |
possibly damaging |
Het |
|
| Other mutations in Ly9 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
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 |
|
R6389:Ly9
|
UTSW |
1 |
171,424,105 (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'- AGACCTGAACAGATGGTCCCAGAAG -3'
(R):5'- AAAGACCTCCACTGGGCGTATGAC -3'
Sequencing Primer
(F):5'- TGGTCCCAGAAGAAAACTGGC -3'
(R):5'- cctctctctctctctctctctc -3'
|
| Posted On |
2013-07-11 |
Incidental Mutation