Incidental Mutation 'R8838:Ly9'
| ID |
674254 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ly9
|
| Ensembl Gene |
ENSMUSG00000004707 |
| Gene Name |
lymphocyte antigen 9 |
| Synonyms |
T100, Lgp100, CD229, SLAMF3 |
| MMRRC Submission |
068666-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R8838 (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 171421569 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 561
(Y561H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000069319
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004827]
[ENSMUST00000068878]
[ENSMUST00000111277]
[ENSMUST00000143463]
[ENSMUST00000194797]
|
| AlphaFold |
Q01965 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000004827
AA Change: Y451H
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: Y451H
| 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: Y561H
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: Y561H
| 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: Y561H
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: Y561H
| 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: 99.7%
- 20x: 99.2%
|
| Validation Efficiency |
100% (52/52) |
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca8a |
T |
A |
11: 109,920,881 (GRCm39) |
I1498F |
probably damaging |
Het |
| Aco2 |
T |
A |
15: 81,796,128 (GRCm39) |
N508K |
probably damaging |
Het |
| Aff4 |
T |
C |
11: 53,297,465 (GRCm39) |
S896P |
possibly damaging |
Het |
| Anapc2 |
T |
G |
2: 25,163,546 (GRCm39) |
V261G |
probably benign |
Het |
| Atm |
A |
G |
9: 53,427,851 (GRCm39) |
S420P |
probably damaging |
Het |
| Bag6 |
C |
T |
17: 35,363,367 (GRCm39) |
R736C |
probably damaging |
Het |
| Brca2 |
A |
G |
5: 150,465,005 (GRCm39) |
T1590A |
possibly damaging |
Het |
| Cacna2d3 |
C |
T |
14: 28,691,220 (GRCm39) |
C35Y |
probably benign |
Het |
| Cep170b |
G |
A |
12: 112,710,159 (GRCm39) |
R1433H |
probably damaging |
Het |
| Cmtm2a |
A |
G |
8: 105,008,036 (GRCm39) |
C138R |
probably damaging |
Het |
| Cntnap5c |
T |
A |
17: 58,198,964 (GRCm39) |
V86E |
|
Het |
| Cog7 |
A |
G |
7: 121,549,106 (GRCm39) |
I385T |
probably damaging |
Het |
| Col28a1 |
A |
T |
6: 8,091,839 (GRCm39) |
|
probably null |
Het |
| Dkk3 |
T |
C |
7: 111,717,542 (GRCm39) |
E309G |
probably benign |
Het |
| Dnah10 |
T |
C |
5: 124,842,614 (GRCm39) |
V1411A |
probably benign |
Het |
| Enox1 |
G |
T |
14: 77,819,950 (GRCm39) |
R235L |
probably benign |
Het |
| Foxn1 |
T |
C |
11: 78,252,438 (GRCm39) |
N317D |
possibly damaging |
Het |
| Grip2 |
G |
A |
6: 91,762,721 (GRCm39) |
|
probably benign |
Het |
| Hmmr |
T |
C |
11: 40,604,854 (GRCm39) |
T406A |
probably benign |
Het |
| Hpcal1 |
G |
A |
12: 17,836,197 (GRCm39) |
R9H |
probably benign |
Het |
| Iglv3 |
A |
T |
16: 19,060,132 (GRCm39) |
Y65* |
probably null |
Het |
| Itgal |
A |
G |
7: 126,910,433 (GRCm39) |
Y514C |
probably damaging |
Het |
| Kcnk9 |
T |
C |
15: 72,418,019 (GRCm39) |
E37G |
possibly damaging |
Het |
| Klhl40 |
A |
G |
9: 121,609,107 (GRCm39) |
D424G |
probably benign |
Het |
| Lbr |
A |
G |
1: 181,648,294 (GRCm39) |
L389P |
possibly damaging |
Het |
| Mcoln3 |
T |
C |
3: 145,845,126 (GRCm39) |
F441L |
probably damaging |
Het |
| Muc20 |
G |
T |
16: 32,613,829 (GRCm39) |
T516K |
possibly damaging |
Het |
| Naa35 |
T |
C |
13: 59,775,775 (GRCm39) |
M551T |
probably benign |
Het |
| Nkx6-2 |
T |
A |
7: 139,161,868 (GRCm39) |
T170S |
probably damaging |
Het |
| Nlrp4c |
T |
A |
7: 6,069,337 (GRCm39) |
F413I |
|
Het |
| Or10w1 |
G |
A |
19: 13,632,371 (GRCm39) |
V193M |
probably damaging |
Het |
| Or1s2 |
C |
A |
19: 13,758,381 (GRCm39) |
T133K |
probably benign |
Het |
| Or6c1b |
T |
G |
10: 129,273,065 (GRCm39) |
L128R |
probably damaging |
Het |
| Or8k22 |
T |
C |
2: 86,163,317 (GRCm39) |
K128E |
possibly damaging |
Het |
| Pcdhga10 |
C |
T |
18: 37,881,952 (GRCm39) |
T571I |
possibly damaging |
Het |
| Pla2g4a |
A |
T |
1: 149,747,256 (GRCm39) |
M310K |
probably benign |
Het |
| Plaa |
T |
C |
4: 94,471,791 (GRCm39) |
T353A |
probably benign |
Het |
| Rapgef1 |
T |
C |
2: 29,627,458 (GRCm39) |
F1172S |
possibly damaging |
Het |
| Rfx2 |
T |
C |
17: 57,087,877 (GRCm39) |
T505A |
possibly damaging |
Het |
| Rfx4 |
T |
C |
10: 84,676,758 (GRCm39) |
V216A |
probably damaging |
Het |
| Rps6kb2 |
G |
T |
19: 4,211,183 (GRCm39) |
A114D |
probably damaging |
Het |
| Sdc2 |
T |
A |
15: 33,023,897 (GRCm39) |
L92* |
probably null |
Het |
| Slc18b1 |
A |
G |
10: 23,696,764 (GRCm39) |
Y319C |
probably benign |
Het |
| Slc22a15 |
A |
T |
3: 101,790,849 (GRCm39) |
Y219N |
probably damaging |
Het |
| Tarbp1 |
A |
T |
8: 127,177,569 (GRCm39) |
|
probably benign |
Het |
| Tfap2d |
T |
C |
1: 19,175,036 (GRCm39) |
L163P |
possibly damaging |
Het |
| Trank1 |
A |
G |
9: 111,193,973 (GRCm39) |
I666V |
probably benign |
Het |
| Trav14-1 |
G |
T |
14: 53,792,009 (GRCm39) |
A120S |
probably damaging |
Het |
| Trps1 |
T |
A |
15: 50,753,007 (GRCm39) |
N20I |
probably benign |
Het |
| Txndc16 |
A |
G |
14: 45,378,028 (GRCm39) |
Y682H |
probably damaging |
Het |
| Ube4a |
A |
T |
9: 44,837,261 (GRCm39) |
D991E |
probably damaging |
Het |
| Zswim4 |
C |
T |
8: 84,940,699 (GRCm39) |
R800Q |
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 |
|
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 |
|
|
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'- TGTAAGAACTTCTCCAGGCCAC -3'
(R):5'- GCCATGGACAATTTTCTGTGC -3'
Sequencing Primer
(F):5'- TTCTCCAGGCCACTAGAGAGTC -3'
(R):5'- TGTGCTCTCCCAACGGTATGAG -3'
|
| Posted On |
2021-07-15 |
Incidental Mutation