Incidental Mutation 'R3819:Ly9'
ID |
274801 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Ly9
|
Ensembl Gene |
ENSMUSG00000004707 |
Gene Name |
lymphocyte antigen 9 |
Synonyms |
T100, Lgp100, CD229, SLAMF3 |
MMRRC Submission |
040773-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R3819 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
1 |
Chromosomal Location |
171416172-171434917 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
G to T
at 171416653 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Asparagine
at position 537
(T537N)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000004827
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004827]
[ENSMUST00000004829]
[ENSMUST00000068878]
[ENSMUST00000111277]
[ENSMUST00000143463]
[ENSMUST00000194797]
|
AlphaFold |
Q01965 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000004827
AA Change: T537N
PolyPhen 2
Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000004827 Gene: ENSMUSG00000004707 AA Change: T537N
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: ENSMUST00000004829
|
SMART Domains |
Protein: ENSMUSP00000004829 Gene: ENSMUSG00000004709
Domain | Start | End | E-Value | Type |
IG
|
26 |
128 |
4.23e-2 |
SMART |
Blast:IG_like
|
146 |
222 |
8e-19 |
BLAST |
transmembrane domain
|
226 |
248 |
N/A |
INTRINSIC |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000068878
AA Change: T647N
PolyPhen 2
Score 0.897 (Sensitivity: 0.82; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000069319 Gene: ENSMUSG00000004707 AA Change: T647N
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
|
SMART Domains |
Protein: ENSMUSP00000106908 Gene: ENSMUSG00000004707
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 |
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 |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000195804
|
Meta Mutation Damage Score |
0.1795 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.7%
- 20x: 96.1%
|
Validation Efficiency |
100% (38/38) |
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: 38 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Aak1 |
T |
C |
6: 86,936,024 (GRCm39) |
|
probably benign |
Het |
Atp1b1 |
C |
T |
1: 164,270,874 (GRCm39) |
R35H |
probably benign |
Het |
Barx1 |
T |
C |
13: 48,818,960 (GRCm39) |
I200T |
possibly damaging |
Het |
Coil |
T |
C |
11: 88,872,619 (GRCm39) |
F380L |
probably benign |
Het |
Csmd1 |
C |
T |
8: 16,052,522 (GRCm39) |
A2201T |
probably damaging |
Het |
Dab2ip |
T |
C |
2: 35,603,222 (GRCm39) |
C417R |
probably damaging |
Het |
Dhx57 |
A |
G |
17: 80,572,503 (GRCm39) |
|
probably null |
Het |
Gabrg3 |
G |
A |
7: 57,031,412 (GRCm39) |
Q43* |
probably null |
Het |
Gbp7 |
C |
A |
3: 142,249,826 (GRCm39) |
H432Q |
possibly damaging |
Het |
Gjb2 |
A |
G |
14: 57,337,530 (GRCm39) |
V226A |
probably benign |
Het |
Gsdme |
A |
C |
6: 50,196,391 (GRCm39) |
S340A |
probably benign |
Het |
Hivep2 |
T |
C |
10: 14,019,685 (GRCm39) |
V2152A |
possibly damaging |
Het |
Hjurp |
G |
C |
1: 88,204,937 (GRCm39) |
|
probably benign |
Het |
Kcnd3 |
C |
T |
3: 105,566,082 (GRCm39) |
A421V |
probably damaging |
Het |
Krt34 |
T |
C |
11: 99,930,844 (GRCm39) |
E186G |
probably damaging |
Het |
Msantd4 |
A |
G |
9: 4,385,237 (GRCm39) |
K321E |
probably damaging |
Het |
Or5ac22 |
A |
G |
16: 59,135,434 (GRCm39) |
F112S |
probably damaging |
Het |
Or5p59 |
A |
G |
7: 107,702,705 (GRCm39) |
Y63C |
possibly damaging |
Het |
Or8b12c |
C |
T |
9: 37,715,465 (GRCm39) |
S86L |
probably benign |
Het |
Or8b40 |
A |
T |
9: 38,027,922 (GRCm39) |
T277S |
possibly damaging |
Het |
Or8b55 |
A |
G |
9: 38,727,722 (GRCm39) |
K308E |
possibly damaging |
Het |
Paxbp1 |
A |
C |
16: 90,819,640 (GRCm39) |
|
probably benign |
Het |
Plcl1 |
T |
A |
1: 55,735,758 (GRCm39) |
D366E |
probably benign |
Het |
Pramel22 |
T |
A |
4: 143,382,365 (GRCm39) |
E110D |
probably benign |
Het |
Prdm5 |
T |
C |
6: 65,913,041 (GRCm39) |
F391L |
possibly damaging |
Het |
Rasef |
C |
G |
4: 73,677,942 (GRCm39) |
D95H |
probably damaging |
Het |
Rufy4 |
T |
C |
1: 74,186,822 (GRCm39) |
C537R |
probably damaging |
Het |
Skint3 |
A |
T |
4: 112,113,085 (GRCm39) |
I232F |
possibly damaging |
Het |
Slc43a3 |
T |
C |
2: 84,774,896 (GRCm39) |
I158T |
probably damaging |
Het |
Smad1 |
G |
A |
8: 80,070,359 (GRCm39) |
A393V |
probably benign |
Het |
Sorl1 |
A |
G |
9: 41,975,345 (GRCm39) |
L487P |
possibly damaging |
Het |
Sspo |
A |
T |
6: 48,458,037 (GRCm39) |
E3269V |
possibly damaging |
Het |
Stat3 |
C |
T |
11: 100,789,459 (GRCm39) |
S377N |
probably damaging |
Het |
Tbpl2 |
A |
G |
2: 23,966,024 (GRCm39) |
V321A |
probably damaging |
Het |
Tnfrsf11a |
C |
T |
1: 105,737,085 (GRCm39) |
T64I |
probably damaging |
Het |
Ttn |
T |
C |
2: 76,729,047 (GRCm39) |
|
probably benign |
Het |
Wdr37 |
A |
G |
13: 8,903,632 (GRCm39) |
|
probably benign |
Het |
Xdh |
A |
T |
17: 74,213,720 (GRCm39) |
I811K |
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 |
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'- TCTGCCTGACCTGTGAATGG -3'
(R):5'- AGCACATGGTCCTTAGCACTG -3'
Sequencing Primer
(F):5'- ACCTGTGAATGGGCTCATG -3'
(R):5'- ATGGTCCTTAGCACTGGGACTC -3'
|
Posted On |
2015-04-02 |