Incidental Mutation 'R6457:Ly9'
| ID |
516501 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ly9
|
| Ensembl Gene |
ENSMUSG00000004707 |
| Gene Name |
lymphocyte antigen 9 |
| Synonyms |
T100, Lgp100, CD229, SLAMF3 |
| MMRRC Submission |
044592-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R6457 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
171416172-171434917 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 171416663 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 644
(S644P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000069319
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004827]
[ENSMUST00000004829]
[ENSMUST00000068878]
[ENSMUST00000111277]
[ENSMUST00000143463]
[ENSMUST00000194797]
|
| AlphaFold |
Q01965 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000004827
AA Change: S534P
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: S534P
| 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 |
probably damaging
Transcript: ENSMUST00000068878
AA Change: S644P
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: S644P
| 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
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.1%
- 20x: 94.3%
|
| Validation Efficiency |
97% (63/65) |
| 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: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110002E22Rik |
T |
A |
3: 137,772,383 (GRCm39) |
V524E |
probably damaging |
Het |
| Acer2 |
T |
A |
4: 86,818,808 (GRCm39) |
M152K |
probably damaging |
Het |
| Actn3 |
T |
C |
19: 4,921,876 (GRCm39) |
D130G |
probably damaging |
Het |
| Ank1 |
T |
A |
8: 23,577,983 (GRCm39) |
F211Y |
probably damaging |
Het |
| Ankfn1 |
C |
T |
11: 89,282,670 (GRCm39) |
A326T |
probably benign |
Het |
| Ankrd11 |
G |
A |
8: 123,635,503 (GRCm39) |
R44C |
probably damaging |
Het |
| Ankrd46 |
A |
G |
15: 36,484,217 (GRCm39) |
|
probably benign |
Het |
| Aurkb |
G |
A |
11: 68,939,172 (GRCm39) |
E132K |
possibly damaging |
Het |
| Bsdc1 |
C |
T |
4: 129,359,069 (GRCm39) |
T9I |
possibly damaging |
Het |
| Card14 |
C |
T |
11: 119,230,428 (GRCm39) |
R767* |
probably null |
Het |
| Ccdc82 |
T |
A |
9: 13,272,745 (GRCm39) |
F411L |
possibly damaging |
Het |
| Col12a1 |
C |
T |
9: 79,552,973 (GRCm39) |
G2106D |
probably damaging |
Het |
| Col27a1 |
T |
A |
4: 63,237,701 (GRCm39) |
|
probably benign |
Het |
| Cox10 |
A |
G |
11: 63,855,198 (GRCm39) |
L361P |
probably damaging |
Het |
| Cox18 |
A |
G |
5: 90,371,548 (GRCm39) |
I84T |
probably benign |
Het |
| Dhrs3 |
T |
C |
4: 144,646,522 (GRCm39) |
S125P |
probably damaging |
Het |
| Fbxl15 |
A |
G |
19: 46,317,765 (GRCm39) |
H149R |
probably benign |
Het |
| Flg2 |
T |
A |
3: 93,127,789 (GRCm39) |
S2234T |
unknown |
Het |
| Gtf2e1 |
A |
C |
16: 37,356,698 (GRCm39) |
|
probably null |
Het |
| H2-Q7 |
A |
T |
17: 35,658,655 (GRCm39) |
S98C |
probably damaging |
Het |
| Hcn2 |
G |
T |
10: 79,569,607 (GRCm39) |
E536* |
probably null |
Het |
| Kat6b |
A |
T |
14: 21,720,748 (GRCm39) |
H1700L |
probably damaging |
Het |
| Klhl3 |
C |
T |
13: 58,248,192 (GRCm39) |
V35I |
probably benign |
Het |
| Krt34 |
A |
T |
11: 99,930,916 (GRCm39) |
L162Q |
probably damaging |
Het |
| Magi1 |
A |
T |
6: 93,676,620 (GRCm39) |
V685E |
probably damaging |
Het |
| Malrd1 |
A |
G |
2: 15,531,408 (GRCm39) |
|
probably benign |
Het |
| Malrd1 |
A |
T |
2: 15,672,740 (GRCm39) |
H599L |
probably benign |
Het |
| Matn2 |
T |
A |
15: 34,426,380 (GRCm39) |
C631S |
probably damaging |
Het |
| Megf8 |
A |
T |
7: 25,049,120 (GRCm39) |
D1739V |
probably damaging |
Het |
| Mlf1 |
G |
A |
3: 67,300,277 (GRCm39) |
R98Q |
probably benign |
Het |
| Mprip |
T |
A |
11: 59,649,815 (GRCm39) |
I1173K |
possibly damaging |
Het |
| Mrc1 |
A |
G |
2: 14,275,016 (GRCm39) |
D439G |
probably damaging |
Het |
| Mroh5 |
A |
T |
15: 73,662,691 (GRCm39) |
W208R |
probably damaging |
Het |
| Ms4a5 |
T |
G |
19: 11,256,646 (GRCm39) |
I84L |
probably benign |
Het |
| Myt1 |
G |
A |
2: 181,405,218 (GRCm39) |
|
probably null |
Het |
| Nbea |
T |
A |
3: 55,907,990 (GRCm39) |
H1374L |
probably damaging |
Het |
| Nbeal1 |
T |
A |
1: 60,292,633 (GRCm39) |
I1095K |
probably benign |
Het |
| Nolc1 |
A |
G |
19: 46,071,509 (GRCm39) |
|
probably benign |
Het |
| Nr5a2 |
A |
G |
1: 136,887,976 (GRCm39) |
L18P |
probably benign |
Het |
| Nup188 |
G |
T |
2: 30,212,199 (GRCm39) |
C562F |
probably damaging |
Het |
| Obscn |
A |
G |
11: 58,971,597 (GRCm39) |
V2415A |
probably damaging |
Het |
| Pacsin2 |
A |
T |
15: 83,263,879 (GRCm39) |
|
probably null |
Het |
| Pias3 |
A |
G |
3: 96,606,839 (GRCm39) |
H34R |
possibly damaging |
Het |
| Ppfia2 |
T |
C |
10: 106,729,361 (GRCm39) |
V903A |
probably damaging |
Het |
| Pramel1 |
T |
A |
4: 143,123,275 (GRCm39) |
L84Q |
probably damaging |
Het |
| Pramel6 |
G |
A |
2: 87,339,782 (GRCm39) |
C182Y |
probably damaging |
Het |
| Prdm4 |
A |
G |
10: 85,743,896 (GRCm39) |
Y120H |
probably damaging |
Het |
| Prss28 |
A |
G |
17: 25,530,331 (GRCm39) |
M212V |
probably benign |
Het |
| Rbp3 |
G |
T |
14: 33,677,224 (GRCm39) |
G391* |
probably null |
Het |
| Rc3h2 |
C |
T |
2: 37,301,151 (GRCm39) |
|
probably null |
Het |
| Ret |
A |
G |
6: 118,150,582 (GRCm39) |
F645L |
probably benign |
Het |
| Saxo5 |
T |
C |
8: 3,529,268 (GRCm39) |
L251P |
probably damaging |
Het |
| Sgsm2 |
A |
G |
11: 74,755,995 (GRCm39) |
S402P |
possibly damaging |
Het |
| Shc3 |
T |
A |
13: 51,636,915 (GRCm39) |
|
probably null |
Het |
| Slc25a16 |
A |
G |
10: 62,776,938 (GRCm39) |
N246S |
probably benign |
Het |
| Snrpd1 |
T |
A |
18: 10,623,694 (GRCm39) |
H26Q |
probably benign |
Het |
| Thsd1 |
A |
G |
8: 22,733,363 (GRCm39) |
T137A |
probably damaging |
Het |
| Tnik |
A |
T |
3: 28,593,597 (GRCm39) |
H151L |
probably damaging |
Het |
| Tns1 |
T |
A |
1: 73,957,209 (GRCm39) |
K1725N |
probably damaging |
Het |
| Tomm40l |
T |
A |
1: 171,048,161 (GRCm39) |
T147S |
probably damaging |
Het |
| Tomm6 |
G |
T |
17: 47,998,932 (GRCm39) |
|
probably benign |
Het |
| Trp53 |
G |
A |
11: 69,480,440 (GRCm39) |
C272Y |
probably damaging |
Het |
| Trpm7 |
A |
T |
2: 126,649,214 (GRCm39) |
V1492E |
probably benign |
Het |
| Tsen2 |
G |
A |
6: 115,536,592 (GRCm39) |
R116H |
probably benign |
Het |
| Uvrag |
A |
G |
7: 98,555,726 (GRCm39) |
F456S |
probably damaging |
Het |
| Vmn1r86 |
A |
T |
7: 12,836,279 (GRCm39) |
M199K |
possibly damaging |
Het |
| Vmn2r4 |
C |
T |
3: 64,317,378 (GRCm39) |
C120Y |
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 |
|
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'- GCACATGGTCCTTAGCACTG -3'
Sequencing Primer
(F):5'- ACCTGTGAATGGGCTCATG -3'
(R):5'- ATGGTCCTTAGCACTGGGACTC -3'
|
| Posted On |
2018-05-21 |
Incidental Mutation