Incidental Mutation 'R2427:Ly9'
| ID |
250257 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ly9
|
| Ensembl Gene |
ENSMUSG00000004707 |
| Gene Name |
lymphocyte antigen 9 |
| Synonyms |
T100, Lgp100, CD229, SLAMF3 |
| MMRRC Submission |
040389-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2427 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
171416172-171434917 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 171434800 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 31
(I31N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000137924
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004827]
[ENSMUST00000068878]
[ENSMUST00000111277]
[ENSMUST00000143463]
[ENSMUST00000194797]
|
| AlphaFold |
Q01965 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000004827
AA Change: I31N
PolyPhen 2
Score 0.204 (Sensitivity: 0.92; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: I31N
| 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 |
possibly damaging
Transcript: ENSMUST00000068878
AA Change: I31N
PolyPhen 2
Score 0.935 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: I31N
| 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: I31N
PolyPhen 2
Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: I31N
| 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 damaging
Transcript: ENSMUST00000143463
AA Change: I31N
PolyPhen 2
Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000137924
Gene: ENSMUSG00000004707
AA Change: I31N
| 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 |
0.6467 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.0%
|
| Validation Efficiency |
100% (37/37) |
| 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: 37 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ankmy1 |
A |
G |
1: 92,798,529 (GRCm39) |
|
probably null |
Het |
| Atp2a1 |
T |
A |
7: 126,045,755 (GRCm39) |
*995L |
probably null |
Het |
| Axin2 |
T |
A |
11: 108,814,800 (GRCm39) |
N229K |
possibly damaging |
Het |
| Capn13 |
A |
T |
17: 73,633,312 (GRCm39) |
|
probably benign |
Het |
| Ccdc180 |
A |
G |
4: 45,929,545 (GRCm39) |
I1202V |
probably benign |
Het |
| Cep295 |
A |
G |
9: 15,245,534 (GRCm39) |
L974P |
probably damaging |
Het |
| Cers3 |
T |
C |
7: 66,445,541 (GRCm39) |
Y321H |
probably benign |
Het |
| Chrnb4 |
T |
C |
9: 54,942,101 (GRCm39) |
Y391C |
probably benign |
Het |
| Ciao1 |
T |
C |
2: 127,088,611 (GRCm39) |
H104R |
probably damaging |
Het |
| Cldn4 |
A |
T |
5: 134,975,331 (GRCm39) |
V90E |
probably damaging |
Het |
| Crbn |
T |
C |
6: 106,760,433 (GRCm39) |
E253G |
probably damaging |
Het |
| Ctns |
A |
G |
11: 73,087,512 (GRCm39) |
W5R |
probably damaging |
Het |
| Eme1 |
G |
A |
11: 94,541,801 (GRCm39) |
|
probably benign |
Het |
| Fat2 |
T |
A |
11: 55,201,638 (GRCm39) |
T479S |
probably benign |
Het |
| Fbxw25 |
T |
C |
9: 109,481,928 (GRCm39) |
N253D |
probably benign |
Het |
| Fer |
A |
G |
17: 64,264,298 (GRCm39) |
I39V |
probably benign |
Het |
| Fmnl2 |
A |
G |
2: 53,006,991 (GRCm39) |
M768V |
probably damaging |
Het |
| Frg1 |
T |
C |
8: 41,867,903 (GRCm39) |
K24E |
probably damaging |
Het |
| I830077J02Rik |
G |
T |
3: 105,835,320 (GRCm39) |
A19D |
probably damaging |
Het |
| Ighv1-20 |
C |
T |
12: 114,687,692 (GRCm39) |
|
silent |
Het |
| Igsf9 |
A |
G |
1: 172,318,306 (GRCm39) |
S149G |
probably damaging |
Het |
| Klra10 |
T |
A |
6: 130,256,298 (GRCm39) |
I119F |
probably benign |
Het |
| Lrrc4b |
T |
A |
7: 44,111,976 (GRCm39) |
I616N |
probably damaging |
Het |
| Lrrc71 |
T |
C |
3: 87,653,309 (GRCm39) |
T64A |
probably benign |
Het |
| Mef2a |
A |
G |
7: 66,915,808 (GRCm39) |
S165P |
probably damaging |
Het |
| Nol4 |
T |
G |
18: 22,983,755 (GRCm39) |
|
probably benign |
Het |
| Nt5el |
T |
C |
13: 105,246,269 (GRCm39) |
F277L |
probably benign |
Het |
| Plxnd1 |
C |
T |
6: 115,944,709 (GRCm39) |
|
probably null |
Het |
| Rab27b |
T |
C |
18: 70,129,205 (GRCm39) |
T30A |
probably damaging |
Het |
| Rasa4 |
A |
G |
5: 136,130,881 (GRCm39) |
D384G |
probably benign |
Het |
| Slx4 |
G |
A |
16: 3,806,851 (GRCm39) |
L531F |
probably damaging |
Het |
| Tafa4 |
C |
T |
6: 96,991,328 (GRCm39) |
|
probably benign |
Het |
| Tgm1 |
C |
T |
14: 55,949,557 (GRCm39) |
|
probably null |
Het |
| Tpm2 |
T |
C |
4: 43,523,306 (GRCm39) |
N17D |
probably damaging |
Het |
| Tyrp1 |
A |
G |
4: 80,769,108 (GRCm39) |
T134A |
probably benign |
Het |
| Zfand6 |
T |
A |
7: 84,283,498 (GRCm39) |
K35* |
probably null |
Het |
| Zfp648 |
G |
A |
1: 154,080,819 (GRCm39) |
C326Y |
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 |
|
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 |
|
|
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'- ACCTCCTCATGGTGATTCAATG -3'
(R):5'- TCTTCCTGGGACACACATGC -3'
Sequencing Primer
(F):5'- CTCCTCATGGTGATTCAATGTGTTTG -3'
(R):5'- TGCACCACAAACCACGCATG -3'
|
| Posted On |
2014-11-12 |
Incidental Mutation