Incidental Mutation 'R5270:Ly9'
| ID |
400156 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ly9
|
| Ensembl Gene |
ENSMUSG00000004707 |
| Gene Name |
lymphocyte antigen 9 |
| Synonyms |
T100, Lgp100, CD229, SLAMF3 |
| MMRRC Submission |
042835-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5270 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
171416172-171434917 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 171428730 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 297
(T297A)
|
| 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: T187A
PolyPhen 2
Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: T187A
| 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: T297A
PolyPhen 2
Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: T297A
| 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: T297A
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: T297A
| 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 |
|
| Meta Mutation Damage Score |
0.2757 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.6%
|
| Validation Efficiency |
98% (59/60) |
| 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: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acsl5 |
T |
C |
19: 55,282,650 (GRCm39) |
V585A |
possibly damaging |
Het |
| Adam6a |
A |
T |
12: 113,507,747 (GRCm39) |
H40L |
possibly damaging |
Het |
| Adamts20 |
G |
A |
15: 94,180,400 (GRCm39) |
P1752S |
probably benign |
Het |
| Atp5if1 |
A |
G |
4: 132,260,611 (GRCm39) |
F27L |
probably damaging |
Het |
| B230104I21Rik |
A |
G |
4: 154,434,050 (GRCm39) |
|
probably benign |
Het |
| Ciz1 |
C |
A |
2: 32,264,511 (GRCm39) |
|
probably null |
Het |
| Crb1 |
T |
A |
1: 139,164,602 (GRCm39) |
Y1174F |
probably damaging |
Het |
| Csf2rb2 |
A |
T |
15: 78,176,182 (GRCm39) |
|
probably null |
Het |
| Cyp3a25 |
A |
T |
5: 145,918,312 (GRCm39) |
M433K |
probably benign |
Het |
| Dock4 |
A |
G |
12: 40,783,270 (GRCm39) |
I735V |
probably benign |
Het |
| Dpp6 |
C |
T |
5: 27,839,532 (GRCm39) |
S349L |
probably damaging |
Het |
| Epg5 |
T |
A |
18: 78,026,778 (GRCm39) |
N1256K |
possibly damaging |
Het |
| Epha4 |
A |
G |
1: 77,483,244 (GRCm39) |
V255A |
probably damaging |
Het |
| Gabrb1 |
A |
T |
5: 72,265,669 (GRCm39) |
D155V |
probably damaging |
Het |
| Gpr35 |
A |
T |
1: 92,910,299 (GRCm39) |
T4S |
probably benign |
Het |
| Hcrt |
T |
C |
11: 100,652,823 (GRCm39) |
T64A |
probably damaging |
Het |
| Henmt1 |
G |
A |
3: 108,867,530 (GRCm39) |
R355H |
probably benign |
Het |
| Hrh1 |
C |
A |
6: 114,458,179 (GRCm39) |
R487S |
possibly damaging |
Het |
| Ints2 |
T |
C |
11: 86,106,621 (GRCm39) |
S930G |
probably damaging |
Het |
| Irs2 |
G |
A |
8: 11,056,678 (GRCm39) |
Q585* |
probably null |
Het |
| Kcns1 |
C |
A |
2: 164,010,249 (GRCm39) |
R170L |
probably benign |
Het |
| Kdm3b |
T |
C |
18: 34,960,467 (GRCm39) |
S1351P |
probably damaging |
Het |
| M6pr |
G |
A |
6: 122,292,048 (GRCm39) |
D127N |
possibly damaging |
Het |
| Macir |
T |
C |
1: 97,573,720 (GRCm39) |
Q115R |
probably damaging |
Het |
| Nhsl3 |
T |
C |
4: 129,118,005 (GRCm39) |
T208A |
possibly damaging |
Het |
| Nit2 |
G |
A |
16: 56,977,494 (GRCm39) |
P179S |
probably damaging |
Het |
| Per1 |
T |
C |
11: 68,994,424 (GRCm39) |
M516T |
probably benign |
Het |
| Pkdrej |
A |
T |
15: 85,702,528 (GRCm39) |
I1136N |
probably damaging |
Het |
| Pramel27 |
A |
G |
4: 143,578,468 (GRCm39) |
M243V |
probably damaging |
Het |
| Prdm9 |
G |
T |
17: 15,773,625 (GRCm39) |
T257K |
probably benign |
Het |
| Prkdc |
T |
C |
16: 15,552,819 (GRCm39) |
L2085P |
probably damaging |
Het |
| Rasgrf1 |
A |
C |
9: 89,908,747 (GRCm39) |
E1240D |
probably benign |
Het |
| Rrh |
T |
C |
3: 129,606,998 (GRCm39) |
I142V |
probably benign |
Het |
| Saal1 |
G |
T |
7: 46,351,157 (GRCm39) |
|
probably benign |
Het |
| Sdcbp2 |
A |
G |
2: 151,426,812 (GRCm39) |
I70V |
probably benign |
Het |
| Skida1 |
C |
A |
2: 18,052,460 (GRCm39) |
A231S |
probably benign |
Het |
| Smtnl2 |
T |
A |
11: 72,290,743 (GRCm39) |
T401S |
probably benign |
Het |
| Sntb1 |
C |
G |
15: 55,506,191 (GRCm39) |
G461R |
probably damaging |
Het |
| Spag4 |
G |
T |
2: 155,907,853 (GRCm39) |
|
probably benign |
Het |
| Tbc1d9 |
A |
G |
8: 83,960,283 (GRCm39) |
M179V |
probably benign |
Het |
| Tm9sf1 |
G |
T |
14: 55,873,938 (GRCm39) |
T520N |
probably damaging |
Het |
| Tmem163 |
G |
A |
1: 127,419,289 (GRCm39) |
|
probably benign |
Het |
| Vmn1r47 |
A |
T |
6: 89,999,525 (GRCm39) |
Q219L |
probably damaging |
Het |
| Vmn2r104 |
A |
T |
17: 20,258,528 (GRCm39) |
C539S |
probably damaging |
Het |
| Wdr17 |
G |
T |
8: 55,096,221 (GRCm39) |
S1024R |
probably benign |
Het |
| Zc3h4 |
A |
G |
7: 16,168,440 (GRCm39) |
T850A |
unknown |
Het |
| Zfa-ps |
A |
G |
10: 52,419,552 (GRCm39) |
|
noncoding transcript |
Het |
| Zfp146 |
G |
T |
7: 29,861,900 (GRCm39) |
N47K |
probably benign |
Het |
| Zfp353-ps |
G |
T |
8: 42,534,572 (GRCm39) |
|
noncoding transcript |
Het |
| Zfp607a |
A |
T |
7: 27,577,730 (GRCm39) |
K267* |
probably null |
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 |
|
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'- GCTGACTAGCTGTGATAGGG -3'
(R):5'- TCTGACTTCAAACTCAGGAGC -3'
Sequencing Primer
(F):5'- CGAGGGGTACTCACTGTAGAC -3'
(R):5'- TTCAAACTCAGGAGCCTCCAG -3'
|
| Posted On |
2016-07-06 |
Incidental Mutation