Incidental Mutation 'R1598:Ly9'
| ID |
175919 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ly9
|
| Ensembl Gene |
ENSMUSG00000004707 |
| Gene Name |
lymphocyte antigen 9 |
| Synonyms |
T100, Lgp100, CD229, SLAMF3 |
| MMRRC Submission |
039635-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R1598 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
1 |
| Chromosomal Location |
171416172-171434917 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 171424075 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 382
(V382A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000004827
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004827]
[ENSMUST00000068878]
[ENSMUST00000111277]
[ENSMUST00000143463]
[ENSMUST00000194797]
|
| AlphaFold |
Q01965 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000004827
AA Change: V382A
PolyPhen 2
Score 0.032 (Sensitivity: 0.95; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: V382A
| 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 benign
Transcript: ENSMUST00000068878
AA Change: V492A
PolyPhen 2
Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
|
| SMART Domains |
Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: V492A
| 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 benign
Transcript: ENSMUST00000111277
AA Change: V492A
PolyPhen 2
Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)
|
| SMART Domains |
Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: V492A
| 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: 99.0%
- 3x: 98.2%
- 10x: 95.7%
- 20x: 90.9%
|
| 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: 68 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5730455P16Rik |
G |
A |
11: 80,254,838 (GRCm39) |
Q328* |
probably null |
Het |
| Aadacl4fm4 |
T |
A |
4: 144,396,994 (GRCm39) |
K246I |
possibly damaging |
Het |
| Adamts1 |
G |
A |
16: 85,595,399 (GRCm39) |
Q260* |
probably null |
Het |
| Add2 |
A |
T |
6: 86,075,628 (GRCm39) |
Y259F |
probably benign |
Het |
| Bora |
T |
C |
14: 99,305,840 (GRCm39) |
V403A |
probably benign |
Het |
| Ccnl1 |
G |
A |
3: 65,854,191 (GRCm39) |
R477W |
probably damaging |
Het |
| Cdc25a |
CG |
CGG |
9: 109,708,961 (GRCm39) |
|
probably null |
Het |
| Cdr2l |
T |
C |
11: 115,284,203 (GRCm39) |
S180P |
probably damaging |
Het |
| Cep290 |
T |
A |
10: 100,385,191 (GRCm39) |
L1889Q |
probably damaging |
Het |
| Ces4a |
T |
C |
8: 105,869,453 (GRCm39) |
V208A |
probably damaging |
Het |
| Col2a1 |
T |
C |
15: 97,877,131 (GRCm39) |
D1049G |
probably damaging |
Het |
| Coro1a |
A |
T |
7: 126,300,864 (GRCm39) |
N154K |
possibly damaging |
Het |
| Cubn |
T |
A |
2: 13,474,600 (GRCm39) |
R401S |
probably benign |
Het |
| Cul7 |
A |
T |
17: 46,974,017 (GRCm39) |
Q1434L |
probably benign |
Het |
| Dab1 |
C |
T |
4: 104,588,948 (GRCm39) |
A524V |
probably benign |
Het |
| Dars1 |
G |
T |
1: 128,301,709 (GRCm39) |
D308E |
probably benign |
Het |
| Dna2 |
T |
A |
10: 62,797,436 (GRCm39) |
F604I |
probably damaging |
Het |
| Dnah1 |
T |
G |
14: 31,023,219 (GRCm39) |
I1033L |
probably benign |
Het |
| Erlin1 |
T |
C |
19: 44,036,112 (GRCm39) |
E206G |
probably damaging |
Het |
| Esrp2 |
T |
A |
8: 106,859,905 (GRCm39) |
E345D |
probably damaging |
Het |
| Foxa1 |
T |
C |
12: 57,589,473 (GRCm39) |
D249G |
possibly damaging |
Het |
| Ghsr |
C |
A |
3: 27,426,426 (GRCm39) |
L161M |
probably benign |
Het |
| Gm57858 |
C |
T |
3: 36,073,146 (GRCm39) |
A379T |
probably damaging |
Het |
| Gpr155 |
C |
A |
2: 73,200,434 (GRCm39) |
V358F |
probably damaging |
Het |
| H2-Eb2 |
A |
T |
17: 34,553,348 (GRCm39) |
N178I |
probably damaging |
Het |
| Hydin |
T |
A |
8: 111,137,306 (GRCm39) |
I703N |
possibly damaging |
Het |
| Kctd15 |
A |
G |
7: 34,341,417 (GRCm39) |
V170A |
probably damaging |
Het |
| Klhl31 |
A |
T |
9: 77,558,298 (GRCm39) |
Y338F |
possibly damaging |
Het |
| Krt5 |
C |
T |
15: 101,620,876 (GRCm39) |
A124T |
probably benign |
Het |
| Krt72 |
T |
A |
15: 101,688,688 (GRCm39) |
I331F |
probably benign |
Het |
| Lrp1b |
T |
A |
2: 41,401,490 (GRCm39) |
D388V |
probably damaging |
Het |
| Mon2 |
T |
C |
10: 122,852,301 (GRCm39) |
Y1024C |
probably damaging |
Het |
| Myh14 |
A |
G |
7: 44,287,818 (GRCm39) |
F572L |
probably damaging |
Het |
| Myh3 |
A |
T |
11: 66,983,997 (GRCm39) |
D987V |
probably damaging |
Het |
| Ndn |
C |
T |
7: 61,998,256 (GRCm39) |
P34L |
probably benign |
Het |
| Nphp4 |
A |
G |
4: 152,646,547 (GRCm39) |
T1360A |
probably benign |
Het |
| Oog4 |
A |
G |
4: 143,164,571 (GRCm39) |
L320P |
probably damaging |
Het |
| Or4k49 |
G |
T |
2: 111,495,099 (GRCm39) |
S176I |
probably damaging |
Het |
| Or5m9 |
C |
T |
2: 85,877,657 (GRCm39) |
T277I |
probably damaging |
Het |
| Or5w8 |
T |
A |
2: 87,688,095 (GRCm39) |
I192K |
probably benign |
Het |
| Pcnx2 |
T |
C |
8: 126,498,825 (GRCm39) |
N1558S |
probably benign |
Het |
| Pde10a |
A |
G |
17: 9,147,976 (GRCm39) |
E147G |
probably damaging |
Het |
| Pgbd5 |
T |
A |
8: 125,101,026 (GRCm39) |
H410L |
probably benign |
Het |
| Plce1 |
A |
C |
19: 38,709,440 (GRCm39) |
D1098A |
probably damaging |
Het |
| Psg25 |
G |
A |
7: 18,265,928 (GRCm39) |
Q16* |
probably null |
Het |
| Psmd9 |
T |
A |
5: 123,379,980 (GRCm39) |
V133E |
probably damaging |
Het |
| Rabgap1 |
C |
T |
2: 37,451,911 (GRCm39) |
S937F |
probably damaging |
Het |
| Rbck1 |
A |
G |
2: 152,165,090 (GRCm39) |
|
probably null |
Het |
| Rprd2 |
C |
G |
3: 95,726,051 (GRCm39) |
|
probably benign |
Het |
| Rrs1 |
A |
G |
1: 9,616,137 (GRCm39) |
N130S |
probably benign |
Het |
| Scmh1 |
A |
T |
4: 120,372,327 (GRCm39) |
I377F |
possibly damaging |
Het |
| Skor1 |
G |
T |
9: 63,053,286 (GRCm39) |
R228S |
probably damaging |
Het |
| Slc2a4 |
A |
G |
11: 69,835,844 (GRCm39) |
V335A |
probably benign |
Het |
| Slc4a9 |
G |
A |
18: 36,661,424 (GRCm39) |
W62* |
probably null |
Het |
| Styxl2 |
G |
A |
1: 165,937,828 (GRCm39) |
T77I |
probably benign |
Het |
| Taar9 |
G |
T |
10: 23,985,305 (GRCm39) |
A43D |
possibly damaging |
Het |
| Tns4 |
T |
C |
11: 98,961,243 (GRCm39) |
Y645C |
probably damaging |
Het |
| Tpcn2 |
G |
T |
7: 144,830,957 (GRCm39) |
Y129* |
probably null |
Het |
| Trpm3 |
T |
C |
19: 22,710,388 (GRCm39) |
S278P |
possibly damaging |
Het |
| Ttc3 |
T |
C |
16: 94,223,156 (GRCm39) |
W615R |
probably damaging |
Het |
| Ttll5 |
T |
C |
12: 85,910,372 (GRCm39) |
V207A |
probably damaging |
Het |
| Ubr7 |
G |
T |
12: 102,736,153 (GRCm39) |
M358I |
probably damaging |
Het |
| Urb1 |
C |
A |
16: 90,574,328 (GRCm39) |
V918F |
possibly damaging |
Het |
| Vmn2r51 |
G |
A |
7: 9,839,432 (GRCm39) |
T52I |
probably benign |
Het |
| Vmn2r95 |
A |
T |
17: 18,672,575 (GRCm39) |
I771F |
probably benign |
Het |
| Wfdc16 |
T |
C |
2: 164,477,350 (GRCm39) |
S107G |
probably benign |
Het |
| Zmym2 |
A |
G |
14: 57,140,226 (GRCm39) |
T22A |
possibly damaging |
Het |
| Zmym2 |
G |
A |
14: 57,151,524 (GRCm39) |
G470R |
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 |
|
|
R1422:Ly9
|
UTSW |
1 |
171,428,780 (GRCm39) |
missense |
probably damaging |
1.00 |
|
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'- AGTGGTGACAACCAACATCCAAGG -3'
(R):5'- ATGATGACCCTGGGCTCTGGATAC -3'
Sequencing Primer
(F):5'- caaactttagcaggtatgtggg -3'
(R):5'- GGGCTCTGGATACTGCTTCC -3'
|
| Posted On |
2014-04-24 |
Incidental Mutation