Incidental Mutation 'R5996:Ly9'
| ID |
481106 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ly9
|
| Ensembl Gene |
ENSMUSG00000004707 |
| Gene Name |
lymphocyte antigen 9 |
| Synonyms |
T100, Lgp100, CD229, SLAMF3 |
| MMRRC Submission |
044175-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5996 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
171416172-171434917 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 171429396 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamine to Leucine
at position 230
(Q230L)
|
| 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: Q120L
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: Q120L
| 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: Q230L
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: Q230L
| 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: Q230L
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: Q230L
| 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 |
0.4484 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.6%
- 20x: 92.4%
|
| Validation Efficiency |
97% (69/71) |
| 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: 70 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700093K21Rik |
A |
G |
11: 23,468,928 (GRCm39) |
M1T |
probably null |
Het |
| A2m |
T |
A |
6: 121,636,353 (GRCm39) |
W741R |
probably damaging |
Het |
| Abcb8 |
C |
T |
5: 24,605,137 (GRCm39) |
R108C |
possibly damaging |
Het |
| Acan |
A |
G |
7: 78,761,068 (GRCm39) |
T1927A |
probably damaging |
Het |
| Agbl4 |
A |
G |
4: 110,812,869 (GRCm39) |
|
probably null |
Het |
| Bltp1 |
T |
C |
3: 36,985,265 (GRCm39) |
F865S |
probably benign |
Het |
| Ccr8 |
T |
A |
9: 119,923,529 (GRCm39) |
C215S |
probably damaging |
Het |
| Cd209b |
T |
C |
8: 3,968,688 (GRCm39) |
T314A |
probably benign |
Het |
| Cd244a |
T |
G |
1: 171,409,208 (GRCm39) |
|
probably null |
Het |
| Cdh23 |
T |
C |
10: 60,249,356 (GRCm39) |
E849G |
possibly damaging |
Het |
| Cep57 |
A |
G |
9: 13,721,175 (GRCm39) |
V268A |
probably damaging |
Het |
| Clip4 |
T |
C |
17: 72,163,305 (GRCm39) |
S626P |
probably damaging |
Het |
| Col19a1 |
C |
T |
1: 24,367,152 (GRCm39) |
G477R |
probably damaging |
Het |
| Col4a4 |
T |
C |
1: 82,433,449 (GRCm39) |
D1498G |
unknown |
Het |
| Coro6 |
T |
C |
11: 77,357,322 (GRCm39) |
V177A |
probably benign |
Het |
| Crip3 |
T |
C |
17: 46,742,210 (GRCm39) |
S202P |
possibly damaging |
Het |
| Cxcr2 |
T |
C |
1: 74,197,619 (GRCm39) |
C38R |
probably damaging |
Het |
| Cyp4f13 |
C |
T |
17: 33,148,447 (GRCm39) |
G327R |
possibly damaging |
Het |
| Dab2 |
C |
T |
15: 6,464,792 (GRCm39) |
Q415* |
probably null |
Het |
| Dennd5b |
A |
G |
6: 148,969,593 (GRCm39) |
F287L |
probably benign |
Het |
| Dlg4 |
G |
A |
11: 69,908,057 (GRCm39) |
R6K |
probably benign |
Het |
| Edc4 |
A |
G |
8: 106,614,033 (GRCm39) |
K429E |
probably damaging |
Het |
| Fam107b |
T |
A |
2: 3,780,667 (GRCm39) |
|
probably null |
Het |
| Flt4 |
A |
T |
11: 49,541,897 (GRCm39) |
D1360V |
probably damaging |
Het |
| Gm1043 |
A |
T |
5: 37,317,168 (GRCm39) |
|
probably benign |
Het |
| Gm4894 |
A |
T |
9: 49,189,970 (GRCm39) |
I82L |
unknown |
Het |
| Gm7247 |
C |
T |
14: 51,601,805 (GRCm39) |
S26F |
probably benign |
Het |
| Gpr176 |
A |
C |
2: 118,114,385 (GRCm39) |
|
probably null |
Het |
| Gtse1 |
T |
C |
15: 85,748,381 (GRCm39) |
L262P |
probably benign |
Het |
| Il4ra |
T |
C |
7: 125,166,393 (GRCm39) |
W46R |
probably damaging |
Het |
| Itga11 |
A |
G |
9: 62,662,955 (GRCm39) |
Y557C |
probably benign |
Het |
| Kcnab2 |
A |
C |
4: 152,519,287 (GRCm39) |
|
probably null |
Het |
| Kcnh7 |
G |
A |
2: 63,014,441 (GRCm39) |
|
probably benign |
Het |
| Map2 |
C |
A |
1: 66,454,043 (GRCm39) |
H978N |
possibly damaging |
Het |
| Map2k6 |
A |
G |
11: 110,388,732 (GRCm39) |
I225V |
possibly damaging |
Het |
| Map3k13 |
A |
G |
16: 21,723,995 (GRCm39) |
N326D |
possibly damaging |
Het |
| Mdga2 |
A |
G |
12: 66,844,537 (GRCm39) |
F85L |
probably benign |
Het |
| Mmp13 |
C |
T |
9: 7,274,269 (GRCm39) |
P192L |
probably damaging |
Het |
| Mrpl37 |
T |
C |
4: 106,923,704 (GRCm39) |
T97A |
probably benign |
Het |
| Mycbpap |
C |
T |
11: 94,404,420 (GRCm39) |
G121D |
probably benign |
Het |
| Nabp1 |
A |
G |
1: 51,510,544 (GRCm39) |
S153P |
probably benign |
Het |
| Nsun3 |
A |
T |
16: 62,590,049 (GRCm39) |
F222I |
probably benign |
Het |
| Or4q3 |
A |
G |
14: 50,582,969 (GRCm39) |
V310A |
possibly damaging |
Het |
| Pcdhga4 |
A |
T |
18: 37,818,991 (GRCm39) |
D180V |
probably benign |
Het |
| Pex6 |
C |
A |
17: 47,025,384 (GRCm39) |
|
probably null |
Het |
| Phrf1 |
C |
A |
7: 140,839,015 (GRCm39) |
|
probably benign |
Het |
| Ppp1r36 |
A |
G |
12: 76,485,936 (GRCm39) |
T365A |
possibly damaging |
Het |
| Ranbp10 |
A |
G |
8: 106,499,672 (GRCm39) |
M519T |
probably benign |
Het |
| Rfx4 |
G |
A |
10: 84,675,881 (GRCm39) |
W32* |
probably null |
Het |
| Ryr1 |
T |
C |
7: 28,723,666 (GRCm39) |
N4131S |
probably benign |
Het |
| Slc27a6 |
A |
G |
18: 58,745,306 (GRCm39) |
E580G |
possibly damaging |
Het |
| Slc7a14 |
T |
C |
3: 31,263,385 (GRCm39) |
D719G |
probably benign |
Het |
| Slfn9 |
A |
G |
11: 82,878,310 (GRCm39) |
I273T |
possibly damaging |
Het |
| Spice1 |
A |
G |
16: 44,205,037 (GRCm39) |
E781G |
probably benign |
Het |
| Sspo |
C |
T |
6: 48,471,110 (GRCm39) |
P4686S |
possibly damaging |
Het |
| Stab1 |
G |
T |
14: 30,861,508 (GRCm39) |
R2500S |
probably benign |
Het |
| Stox2 |
A |
T |
8: 47,656,182 (GRCm39) |
M98K |
possibly damaging |
Het |
| Tacc2 |
T |
C |
7: 130,225,213 (GRCm39) |
S633P |
probably damaging |
Het |
| Tex51 |
G |
T |
18: 32,595,545 (GRCm39) |
|
probably benign |
Het |
| Tm9sf4 |
T |
C |
2: 153,037,491 (GRCm39) |
|
probably null |
Het |
| Togaram2 |
T |
A |
17: 72,011,778 (GRCm39) |
F486I |
probably damaging |
Het |
| Trappc12 |
A |
G |
12: 28,797,113 (GRCm39) |
S140P |
possibly damaging |
Het |
| Ttc29 |
A |
T |
8: 79,003,525 (GRCm39) |
N247I |
probably damaging |
Het |
| Uso1 |
A |
T |
5: 92,340,589 (GRCm39) |
E668D |
probably benign |
Het |
| Vmn2r69 |
A |
T |
7: 85,061,117 (GRCm39) |
|
probably null |
Het |
| Xirp2 |
T |
A |
2: 67,341,994 (GRCm39) |
L1412I |
possibly damaging |
Het |
| Xrcc5 |
T |
A |
1: 72,349,617 (GRCm39) |
D15E |
probably damaging |
Het |
| Zfp661 |
T |
C |
2: 127,418,968 (GRCm39) |
K391E |
probably damaging |
Het |
| Zfp729b |
A |
G |
13: 67,741,977 (GRCm39) |
I106T |
probably benign |
Het |
| Zfyve9 |
A |
C |
4: 108,576,557 (GRCm39) |
S175A |
probably benign |
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 |
|
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 |
|
|
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'- GGGTTTTCAAGTCTGGCCAG -3'
(R):5'- GAATCTGTGACCCCATCCGATAC -3'
Sequencing Primer
(F):5'- AAGTCTGGCCAGCCTCTCTTAG -3'
(R):5'- GTGACCCCATCCGATACTGATTC -3'
|
| Posted On |
2017-06-26 |
Incidental Mutation