Incidental Mutation 'R1422:Ly9'
ID |
161108 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Ly9
|
Ensembl Gene |
ENSMUSG00000004707 |
Gene Name |
lymphocyte antigen 9 |
Synonyms |
T100, Lgp100, CD229, SLAMF3 |
MMRRC Submission |
039478-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R1422 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
1 |
Chromosomal Location |
171416172-171434917 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 171428780 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Alanine
at position 280
(V280A)
|
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: V170A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000004827 Gene: ENSMUSG00000004707 AA Change: V170A
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: V280A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000069319 Gene: ENSMUSG00000004707 AA Change: V280A
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: V280A
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000106908 Gene: ENSMUSG00000004707 AA Change: V280A
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 |
|
Meta Mutation Damage Score |
0.5954 |
Coding Region Coverage |
- 1x: 98.9%
- 3x: 97.9%
- 10x: 95.2%
- 20x: 89.6%
|
Validation Efficiency |
100% (51/51) |
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: 47 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
2700062C07Rik |
A |
G |
18: 24,610,333 (GRCm39) |
T170A |
probably benign |
Het |
Arhgap5 |
T |
A |
12: 52,566,297 (GRCm39) |
D1089E |
probably damaging |
Het |
Atrn |
T |
C |
2: 130,799,834 (GRCm39) |
Y404H |
probably damaging |
Het |
Becn1 |
T |
C |
11: 101,185,952 (GRCm39) |
D98G |
possibly damaging |
Het |
Coro2b |
A |
G |
9: 62,336,229 (GRCm39) |
|
probably null |
Het |
Cpne4 |
T |
C |
9: 104,777,484 (GRCm39) |
I143T |
probably damaging |
Het |
Cr2 |
A |
G |
1: 194,853,433 (GRCm39) |
I35T |
probably benign |
Het |
Ctns |
T |
C |
11: 73,076,072 (GRCm39) |
Y321C |
probably damaging |
Het |
Cyp4f16 |
A |
T |
17: 32,761,973 (GRCm39) |
M174L |
probably damaging |
Het |
Dpy19l4 |
T |
C |
4: 11,317,168 (GRCm39) |
E10G |
possibly damaging |
Het |
Dtx3 |
T |
A |
10: 127,027,158 (GRCm39) |
I339F |
possibly damaging |
Het |
Fam184a |
A |
T |
10: 53,551,304 (GRCm39) |
M625K |
probably benign |
Het |
Fgd6 |
A |
G |
10: 93,881,234 (GRCm39) |
E696G |
probably damaging |
Het |
Gm17535 |
A |
G |
9: 3,035,804 (GRCm39) |
Y224C |
probably null |
Het |
Gria1 |
T |
A |
11: 57,080,614 (GRCm39) |
L199Q |
probably benign |
Het |
Hk1 |
T |
C |
10: 62,131,873 (GRCm39) |
D184G |
probably null |
Het |
Ift88 |
T |
C |
14: 57,675,758 (GRCm39) |
|
probably benign |
Het |
Ift88 |
G |
A |
14: 57,710,436 (GRCm39) |
V403M |
probably damaging |
Het |
Igsf1 |
C |
A |
X: 48,871,813 (GRCm39) |
G737* |
probably null |
Het |
Kif19a |
A |
G |
11: 114,676,635 (GRCm39) |
D488G |
probably benign |
Het |
Lpcat2 |
T |
C |
8: 93,606,045 (GRCm39) |
L232P |
probably damaging |
Het |
Macrod2 |
T |
A |
2: 140,261,861 (GRCm39) |
|
probably null |
Het |
Mmp1a |
A |
G |
9: 7,464,298 (GRCm39) |
|
probably null |
Het |
Mmrn2 |
A |
G |
14: 34,118,196 (GRCm39) |
H80R |
probably damaging |
Het |
Or2b4 |
T |
C |
17: 38,116,254 (GRCm39) |
Y73H |
probably damaging |
Het |
Or51f23 |
G |
A |
7: 102,453,057 (GRCm39) |
R124H |
probably benign |
Het |
Or5l13 |
G |
A |
2: 87,780,439 (GRCm39) |
T46I |
probably benign |
Het |
Pkd1l3 |
C |
A |
8: 110,348,340 (GRCm39) |
P194H |
unknown |
Het |
Plk2 |
A |
G |
13: 110,536,023 (GRCm39) |
M576V |
probably damaging |
Het |
Pms2 |
T |
A |
5: 143,850,523 (GRCm39) |
S113T |
probably damaging |
Het |
Ptprk |
A |
G |
10: 28,351,276 (GRCm39) |
I590V |
possibly damaging |
Het |
Ptpro |
T |
A |
6: 137,420,592 (GRCm39) |
V1007D |
probably damaging |
Het |
Pwwp4a |
G |
T |
X: 72,171,261 (GRCm39) |
G218C |
probably damaging |
Het |
Rad17 |
A |
G |
13: 100,781,590 (GRCm39) |
L69P |
probably benign |
Het |
Rmc1 |
G |
A |
18: 12,314,680 (GRCm39) |
D87N |
probably damaging |
Het |
Robo2 |
G |
A |
16: 73,775,336 (GRCm39) |
T466M |
probably damaging |
Het |
Sema6a |
A |
G |
18: 47,439,498 (GRCm39) |
C9R |
probably benign |
Het |
Slc6a19 |
A |
G |
13: 73,833,988 (GRCm39) |
S357P |
probably benign |
Het |
Spata31e2 |
C |
G |
1: 26,721,547 (GRCm39) |
S1211T |
possibly damaging |
Het |
Spock3 |
T |
C |
8: 63,597,023 (GRCm39) |
I109T |
possibly damaging |
Het |
Svs6 |
T |
C |
2: 164,159,580 (GRCm39) |
|
probably null |
Het |
Tenm4 |
A |
T |
7: 96,199,258 (GRCm39) |
D17V |
probably damaging |
Het |
Trp53bp2 |
T |
A |
1: 182,274,029 (GRCm39) |
M558K |
probably benign |
Het |
Ttn |
T |
C |
2: 76,572,014 (GRCm39) |
E26293G |
probably damaging |
Het |
Vmn1r29 |
A |
G |
6: 58,284,871 (GRCm39) |
Y197C |
probably damaging |
Het |
Wdfy3 |
A |
T |
5: 102,032,080 (GRCm39) |
|
probably benign |
Het |
Zfp366 |
A |
G |
13: 99,365,804 (GRCm39) |
K322E |
probably 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 |
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 |
|
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'- TGAGCTGACTAGCTGTGATAGGGAG -3'
(R):5'- AGGCAGAAGCTGCAATGTCTCATC -3'
Sequencing Primer
(F):5'- AAATGTCTCACACTGGGGTC -3'
(R):5'- TCTCTGACTTCAAACTCAGGAGC -3'
|
Posted On |
2014-03-14 |