Incidental Mutation 'R6732:Ly9'
| ID |
530090 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ly9
|
| Ensembl Gene |
ENSMUSG00000004707 |
| Gene Name |
lymphocyte antigen 9 |
| Synonyms |
T100, Lgp100, CD229, SLAMF3 |
| MMRRC Submission |
044850-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R6732 (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 C
at 171421653 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 533
(T533A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000106908
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004827]
[ENSMUST00000068878]
[ENSMUST00000111277]
[ENSMUST00000143463]
[ENSMUST00000194797]
|
| AlphaFold |
Q01965 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000004827
AA Change: T423A
PolyPhen 2
Score 0.622 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: T423A
| 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: T533A
PolyPhen 2
Score 0.448 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: T533A
| 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 |
possibly damaging
Transcript: ENSMUST00000111277
AA Change: T533A
PolyPhen 2
Score 0.739 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: T533A
| 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 |
|
| Meta Mutation Damage Score |
0.1712 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.3%
- 20x: 95.5%
|
| Validation Efficiency |
98% (43/44) |
| 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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb11 |
A |
G |
2: 69,117,190 (GRCm39) |
I486T |
probably damaging |
Het |
| Abcc5 |
T |
C |
16: 20,223,434 (GRCm39) |
N158S |
probably benign |
Het |
| AI182371 |
G |
T |
2: 34,974,717 (GRCm39) |
|
probably benign |
Het |
| Ap1ar |
G |
A |
3: 127,609,334 (GRCm39) |
Q96* |
probably null |
Het |
| Cd101 |
C |
T |
3: 100,915,515 (GRCm39) |
S684N |
probably benign |
Het |
| Cdh16 |
T |
G |
8: 105,345,165 (GRCm39) |
I375L |
probably benign |
Het |
| Chchd6 |
A |
G |
6: 89,551,436 (GRCm39) |
V75A |
probably benign |
Het |
| Coro2a |
A |
T |
4: 46,551,374 (GRCm39) |
N110K |
probably damaging |
Het |
| Cyp2c69 |
A |
G |
19: 39,869,943 (GRCm39) |
V93A |
probably benign |
Het |
| Dnaaf9 |
A |
G |
2: 130,652,740 (GRCm39) |
|
probably null |
Het |
| Egln3 |
C |
T |
12: 54,227,427 (GRCm39) |
A235T |
probably benign |
Het |
| Fryl |
T |
C |
5: 73,212,124 (GRCm39) |
T2335A |
probably damaging |
Het |
| Fzd3 |
T |
C |
14: 65,473,252 (GRCm39) |
D172G |
probably benign |
Het |
| Galnt2 |
T |
A |
8: 125,067,561 (GRCm39) |
W447R |
probably damaging |
Het |
| Iqce |
A |
G |
5: 140,660,990 (GRCm39) |
L450P |
probably benign |
Het |
| Map3k19 |
A |
C |
1: 127,751,969 (GRCm39) |
F257V |
probably benign |
Het |
| Mroh7 |
GTT |
GTTT |
4: 106,537,910 (GRCm39) |
|
probably null |
Het |
| Or5ac20 |
A |
T |
16: 59,104,314 (GRCm39) |
V182E |
probably benign |
Het |
| Pcdhb11 |
A |
T |
18: 37,555,197 (GRCm39) |
I176F |
probably benign |
Het |
| Pigp |
A |
C |
16: 94,166,300 (GRCm39) |
L96R |
probably damaging |
Het |
| Pkd1 |
A |
G |
17: 24,788,387 (GRCm39) |
D715G |
probably damaging |
Het |
| Plxnd1 |
A |
C |
6: 115,946,890 (GRCm39) |
L828R |
possibly damaging |
Het |
| Pramel15 |
C |
T |
4: 144,099,743 (GRCm39) |
V341I |
probably benign |
Het |
| Psmd2 |
T |
A |
16: 20,481,386 (GRCm39) |
S814T |
probably benign |
Het |
| Pusl1 |
A |
G |
4: 155,975,573 (GRCm39) |
S87P |
probably benign |
Het |
| Rgs3 |
T |
A |
4: 62,521,180 (GRCm39) |
D34E |
probably benign |
Het |
| Rhof |
A |
G |
5: 123,269,999 (GRCm39) |
F53L |
probably damaging |
Het |
| Sik3 |
C |
A |
9: 46,123,851 (GRCm39) |
P1217T |
probably benign |
Het |
| Skic2 |
G |
A |
17: 35,064,166 (GRCm39) |
R507* |
probably null |
Het |
| Slc14a2 |
A |
G |
18: 78,235,389 (GRCm39) |
Y263H |
probably damaging |
Het |
| Slc26a4 |
C |
T |
12: 31,576,599 (GRCm39) |
|
probably null |
Het |
| Smyd3 |
T |
G |
1: 179,223,395 (GRCm39) |
H178P |
probably benign |
Het |
| Thada |
T |
C |
17: 84,761,842 (GRCm39) |
|
probably null |
Het |
| Top1mt |
A |
C |
15: 75,541,337 (GRCm39) |
|
probably null |
Het |
| Trim17 |
A |
T |
11: 58,861,851 (GRCm39) |
|
probably null |
Het |
| Ttn |
A |
T |
2: 76,770,395 (GRCm39) |
F2599I |
possibly damaging |
Het |
| Tuba3a |
A |
T |
6: 125,258,608 (GRCm39) |
D127E |
probably benign |
Het |
| Ucp1 |
A |
G |
8: 84,018,106 (GRCm39) |
T68A |
probably benign |
Het |
| Vmn2r69 |
A |
G |
7: 85,060,351 (GRCm39) |
V411A |
probably benign |
Het |
| Vmn2r74 |
A |
T |
7: 85,606,758 (GRCm39) |
V196E |
probably damaging |
Het |
| Wdr59 |
T |
C |
8: 112,227,684 (GRCm39) |
Y131C |
probably damaging |
Het |
| Yod1 |
G |
A |
1: 130,645,275 (GRCm39) |
G19S |
probably damaging |
Het |
| Zbtb21 |
G |
T |
16: 97,752,282 (GRCm39) |
S667Y |
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 |
|
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 |
|
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'- ACCCATCCACTTTATCATATGGAG -3'
(R):5'- CCCAGCCTTGTGATCTGATC -3'
Sequencing Primer
(F):5'- CCACTTTATCATATGGAGTGATTGC -3'
(R):5'- CCTTGTGATCTGATCTAGGACAGAAG -3'
|
| Posted On |
2018-08-01 |
Incidental Mutation