Incidental Mutation 'R6866:Ly9'
| ID |
535895 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ly9
|
| Ensembl Gene |
ENSMUSG00000004707 |
| Gene Name |
lymphocyte antigen 9 |
| Synonyms |
T100, Lgp100, CD229, SLAMF3 |
| MMRRC Submission |
044965-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R6866 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
1 |
| Chromosomal Location |
171416172-171434917 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 171432847 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Methionine
at position 55
(I55M)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000106908
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004827]
[ENSMUST00000068878]
[ENSMUST00000111277]
[ENSMUST00000143463]
[ENSMUST00000194797]
|
| AlphaFold |
Q01965 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000004827
|
| SMART Domains |
Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
| 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: I55M
PolyPhen 2
Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: I55M
| 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: I55M
PolyPhen 2
Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: I55M
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.3%
- 20x: 97.7%
|
| 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: 62 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Alms1 |
A |
G |
6: 85,598,080 (GRCm39) |
T1438A |
possibly damaging |
Het |
| Als2 |
T |
A |
1: 59,250,292 (GRCm39) |
Q484L |
probably damaging |
Het |
| Apeh |
G |
A |
9: 107,969,878 (GRCm39) |
H186Y |
probably damaging |
Het |
| Bcl2l13 |
T |
A |
6: 120,839,850 (GRCm39) |
N49K |
probably benign |
Het |
| Bptf |
T |
C |
11: 106,964,406 (GRCm39) |
D1596G |
probably damaging |
Het |
| Brsk1 |
T |
C |
7: 4,709,406 (GRCm39) |
M325T |
probably damaging |
Het |
| Caly |
T |
C |
7: 139,650,532 (GRCm39) |
M137V |
probably benign |
Het |
| Cdca2 |
T |
C |
14: 67,931,115 (GRCm39) |
E526G |
possibly damaging |
Het |
| Cnga4 |
A |
G |
7: 105,056,952 (GRCm39) |
S352G |
possibly damaging |
Het |
| Cntnap5c |
A |
C |
17: 58,399,289 (GRCm39) |
T381P |
probably benign |
Het |
| Cr2 |
T |
A |
1: 194,833,999 (GRCm39) |
Y633F |
probably damaging |
Het |
| Cryba1 |
T |
C |
11: 77,610,355 (GRCm39) |
N120S |
probably benign |
Het |
| Cyfip2 |
G |
A |
11: 46,133,286 (GRCm39) |
R805* |
probably null |
Het |
| Dnah7c |
C |
A |
1: 46,696,403 (GRCm39) |
P2095Q |
probably damaging |
Het |
| Eif3k |
T |
C |
7: 28,676,651 (GRCm39) |
E110G |
possibly damaging |
Het |
| Extl2 |
T |
A |
3: 115,821,002 (GRCm39) |
M283K |
probably damaging |
Het |
| Extl2 |
A |
G |
3: 115,821,001 (GRCm39) |
M283V |
probably damaging |
Het |
| Focad |
T |
C |
4: 88,321,623 (GRCm39) |
I1658T |
probably benign |
Het |
| Fstl5 |
A |
T |
3: 76,229,532 (GRCm39) |
H111L |
probably damaging |
Het |
| Garnl3 |
A |
G |
2: 32,892,785 (GRCm39) |
|
probably null |
Het |
| Gm3633 |
T |
A |
14: 42,462,579 (GRCm39) |
|
probably benign |
Het |
| Il4i1 |
T |
A |
7: 44,485,963 (GRCm39) |
|
probably null |
Het |
| Kcnj6 |
A |
T |
16: 94,563,536 (GRCm39) |
C321S |
probably damaging |
Het |
| Kif20a |
A |
T |
18: 34,761,546 (GRCm39) |
Y313F |
probably benign |
Het |
| Kmt2d |
T |
G |
15: 98,755,274 (GRCm39) |
|
probably benign |
Het |
| Kynu |
T |
A |
2: 43,453,122 (GRCm39) |
Y48* |
probably null |
Het |
| Mgme1 |
T |
C |
2: 144,118,439 (GRCm39) |
V237A |
probably damaging |
Het |
| Mmp16 |
T |
A |
4: 17,853,800 (GRCm39) |
L27H |
probably benign |
Het |
| Mtres1 |
ACTGCACCACCT |
ACT |
10: 43,408,721 (GRCm39) |
|
probably benign |
Het |
| Myh1 |
A |
C |
11: 67,115,219 (GRCm39) |
D1918A |
probably damaging |
Het |
| Myo5a |
G |
A |
9: 75,047,970 (GRCm39) |
C266Y |
probably damaging |
Het |
| Nckap5l |
A |
G |
15: 99,324,349 (GRCm39) |
I718T |
probably benign |
Het |
| Nptx1 |
A |
G |
11: 119,437,476 (GRCm39) |
|
probably null |
Het |
| Or56a42-ps1 |
T |
A |
7: 104,775,825 (GRCm39) |
M228L |
probably benign |
Het |
| Or5k16 |
A |
G |
16: 58,736,351 (GRCm39) |
Y218H |
probably damaging |
Het |
| Or5p76 |
A |
G |
7: 108,122,377 (GRCm39) |
F260S |
probably damaging |
Het |
| Phc3 |
T |
A |
3: 30,968,680 (GRCm39) |
K783* |
probably null |
Het |
| Pkdrej |
A |
T |
15: 85,705,082 (GRCm39) |
C285S |
probably damaging |
Het |
| Pot1b |
T |
A |
17: 55,960,474 (GRCm39) |
T619S |
possibly damaging |
Het |
| Pramel32 |
T |
A |
4: 88,545,977 (GRCm39) |
D455V |
probably damaging |
Het |
| Psg21 |
A |
T |
7: 18,386,209 (GRCm39) |
V259E |
probably damaging |
Het |
| Pvr |
A |
C |
7: 19,652,555 (GRCm39) |
I120S |
probably benign |
Het |
| Rbm17 |
T |
G |
2: 11,602,901 (GRCm39) |
I68L |
probably benign |
Het |
| Rnf138 |
C |
T |
18: 21,135,199 (GRCm39) |
P28L |
probably damaging |
Het |
| Rnf207 |
C |
T |
4: 152,396,989 (GRCm39) |
C385Y |
possibly damaging |
Het |
| Serping1 |
A |
C |
2: 84,600,577 (GRCm39) |
V255G |
probably benign |
Het |
| Slc25a3 |
A |
T |
10: 90,955,567 (GRCm39) |
V91E |
probably damaging |
Het |
| Slc26a8 |
T |
C |
17: 28,857,455 (GRCm39) |
D896G |
probably benign |
Het |
| Slc27a5 |
T |
A |
7: 12,731,443 (GRCm39) |
T183S |
probably benign |
Het |
| Slc33a1 |
A |
T |
3: 63,850,744 (GRCm39) |
F527I |
probably benign |
Het |
| Sting1 |
T |
C |
18: 35,872,482 (GRCm39) |
H50R |
probably damaging |
Het |
| Strn4 |
A |
T |
7: 16,562,710 (GRCm39) |
D283V |
probably damaging |
Het |
| Sult1e1 |
G |
A |
5: 87,734,625 (GRCm39) |
T107I |
probably damaging |
Het |
| Tango6 |
G |
A |
8: 107,469,104 (GRCm39) |
|
probably null |
Het |
| Tecrl |
G |
T |
5: 83,461,161 (GRCm39) |
P99T |
probably damaging |
Het |
| Ticrr |
T |
C |
7: 79,343,705 (GRCm39) |
L1190P |
possibly damaging |
Het |
| Timm50 |
C |
T |
7: 28,005,370 (GRCm39) |
R349H |
probably damaging |
Het |
| Tjp2 |
A |
G |
19: 24,079,355 (GRCm39) |
I840T |
probably damaging |
Het |
| Tmem45a2 |
T |
A |
16: 56,867,386 (GRCm39) |
N105I |
probably damaging |
Het |
| Tsbp1 |
T |
A |
17: 34,678,935 (GRCm39) |
C216S |
possibly damaging |
Het |
| Zfp148 |
T |
A |
16: 33,288,496 (GRCm39) |
C162S |
probably damaging |
Het |
| Zfp534 |
T |
C |
4: 147,758,938 (GRCm39) |
K577R |
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 |
|
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 |
|
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 |
|
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'- GAGCATGGTAGGATCCTGAATCAC -3'
(R):5'- AAGGAGAATGTCTGGTCTCATTC -3'
Sequencing Primer
(F):5'- TACAAGGAGTAGCCATCTTCGCTG -3'
(R):5'- GAGAATGTCTGGTCTCATTCATTTC -3'
|
| Posted On |
2018-10-18 |
Incidental Mutation