Incidental Mutation 'R5203:Ly9'
ID |
398229 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Ly9
|
Ensembl Gene |
ENSMUSG00000004707 |
Gene Name |
lymphocyte antigen 9 |
Synonyms |
T100, Lgp100, CD229, SLAMF3 |
MMRRC Submission |
042778-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R5203 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
1 |
Chromosomal Location |
171416172-171434917 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to A
at 171427347 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Phenylalanine
at position 403
(V403F)
|
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: V293F
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000004827 Gene: ENSMUSG00000004707 AA Change: V293F
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: V403F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000069319 Gene: ENSMUSG00000004707 AA Change: V403F
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: V403F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000106908 Gene: ENSMUSG00000004707 AA Change: V403F
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: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.1%
|
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: 35 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930562C15Rik |
T |
G |
16: 4,653,462 (GRCm39) |
S4A |
unknown |
Het |
Adgrv1 |
A |
T |
13: 81,659,024 (GRCm39) |
N2053K |
possibly damaging |
Het |
Akr1c13 |
C |
T |
13: 4,247,896 (GRCm39) |
R223* |
probably null |
Het |
Arhgef11 |
A |
G |
3: 87,642,664 (GRCm39) |
Y1370C |
probably damaging |
Het |
Arid1a |
T |
C |
4: 133,409,314 (GRCm39) |
E1731G |
unknown |
Het |
Cyp2c54 |
A |
T |
19: 40,060,918 (GRCm39) |
V75E |
probably damaging |
Het |
Fa2h |
A |
G |
8: 112,075,996 (GRCm39) |
M209T |
probably benign |
Het |
Fam171a1 |
T |
C |
2: 3,224,582 (GRCm39) |
I311T |
probably damaging |
Het |
Fat3 |
C |
A |
9: 16,289,438 (GRCm39) |
L28F |
possibly damaging |
Het |
Fntb |
C |
A |
12: 76,884,346 (GRCm39) |
P22Q |
probably benign |
Het |
Gmeb1 |
T |
C |
4: 131,959,320 (GRCm39) |
|
probably null |
Het |
Gpr22 |
A |
G |
12: 31,759,787 (GRCm39) |
S112P |
probably damaging |
Het |
Htr7 |
A |
G |
19: 35,941,792 (GRCm39) |
S464P |
probably benign |
Het |
Igkv4-80 |
A |
C |
6: 68,993,649 (GRCm39) |
S81A |
probably benign |
Het |
Krt79 |
A |
G |
15: 101,838,175 (GRCm39) |
S527P |
unknown |
Het |
Lnpep |
A |
T |
17: 17,757,325 (GRCm39) |
D858E |
probably damaging |
Het |
Mindy4 |
A |
G |
6: 55,232,646 (GRCm39) |
Q363R |
probably benign |
Het |
Mtmr10 |
G |
A |
7: 63,967,909 (GRCm39) |
V273I |
probably benign |
Het |
Mup2 |
T |
A |
4: 60,139,728 (GRCm39) |
E20V |
probably damaging |
Het |
Myo16 |
A |
G |
8: 10,410,995 (GRCm39) |
N151S |
probably damaging |
Het |
Nod2 |
A |
C |
8: 89,391,079 (GRCm39) |
D462A |
probably damaging |
Het |
Nt5c2 |
A |
G |
19: 46,878,247 (GRCm39) |
Y497H |
probably damaging |
Het |
Or12d2 |
A |
T |
17: 37,625,092 (GRCm39) |
L61Q |
probably damaging |
Het |
Or4k44 |
A |
C |
2: 111,367,981 (GRCm39) |
Y218D |
probably damaging |
Het |
Otx1 |
C |
A |
11: 21,947,037 (GRCm39) |
A91S |
probably damaging |
Het |
Pcdhac1 |
A |
T |
18: 37,224,243 (GRCm39) |
D352V |
probably damaging |
Het |
Psap |
A |
G |
10: 60,130,755 (GRCm39) |
D195G |
probably damaging |
Het |
Scyl1 |
G |
A |
19: 5,821,395 (GRCm39) |
|
probably benign |
Het |
Sh3bgr |
A |
G |
16: 96,025,720 (GRCm39) |
|
probably benign |
Het |
Slc2a12 |
G |
T |
10: 22,521,213 (GRCm39) |
|
probably null |
Het |
Slc2a12 |
G |
C |
10: 22,568,117 (GRCm39) |
V515L |
probably benign |
Het |
Ttc17 |
T |
C |
2: 94,209,061 (GRCm39) |
Y131C |
probably damaging |
Het |
Ttc27 |
A |
G |
17: 75,084,649 (GRCm39) |
D419G |
probably damaging |
Het |
Ubxn8 |
T |
C |
8: 34,123,639 (GRCm39) |
E100G |
probably damaging |
Het |
Zpbp |
T |
C |
11: 11,358,451 (GRCm39) |
E272G |
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 |
|
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 |
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'- TCTCTCACTGGCTTTTATAAACAGC -3'
(R):5'- TTCACTGACAGGTCTGGTTCC -3'
Sequencing Primer
(F):5'- GCTTCTATAGCCTGGATGGAAG -3'
(R):5'- ACAGGTCTGGTTCCATGCTG -3'
|
Posted On |
2016-07-06 |