Incidental Mutation 'IGL00090:Ly9'
| ID |
1941 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Ly9
|
| Ensembl Gene |
ENSMUSG00000004707 |
| Gene Name |
lymphocyte antigen 9 |
| Synonyms |
T100, Lgp100, CD229, SLAMF3 |
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
IGL00090
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
1 |
| Chromosomal Location |
171416172-171434917 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 171421019 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 624
(I624N)
|
| 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: I514N
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: I514N
| 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: I624N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: I624N
| 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: I624N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: I624N
| 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 |
|
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb5 |
T |
C |
12: 118,854,345 (GRCm39) |
T857A |
probably benign |
Het |
| Abcc9 |
A |
T |
6: 142,578,916 (GRCm39) |
|
probably benign |
Het |
| Adam11 |
A |
G |
11: 102,667,657 (GRCm39) |
T709A |
probably benign |
Het |
| Adgre1 |
A |
G |
17: 57,757,055 (GRCm39) |
I771V |
probably benign |
Het |
| Adgrv1 |
T |
G |
13: 81,553,527 (GRCm39) |
|
probably null |
Het |
| Adgrv1 |
C |
T |
13: 81,726,220 (GRCm39) |
D602N |
probably damaging |
Het |
| Adra1d |
G |
T |
2: 131,403,597 (GRCm39) |
D164E |
possibly damaging |
Het |
| Ago3 |
A |
G |
4: 126,265,334 (GRCm39) |
L319P |
probably damaging |
Het |
| Aim2 |
A |
G |
1: 173,283,031 (GRCm39) |
S38G |
probably benign |
Het |
| Apoh |
A |
G |
11: 108,286,660 (GRCm39) |
D28G |
probably benign |
Het |
| Atm |
C |
T |
9: 53,435,743 (GRCm39) |
R189K |
probably damaging |
Het |
| Bbs1 |
T |
C |
19: 4,943,038 (GRCm39) |
T451A |
probably benign |
Het |
| BC034090 |
T |
C |
1: 155,101,193 (GRCm39) |
D719G |
possibly damaging |
Het |
| Bcr |
T |
C |
10: 74,992,903 (GRCm39) |
|
probably benign |
Het |
| Bmp2 |
A |
T |
2: 133,402,947 (GRCm39) |
Q166L |
probably benign |
Het |
| Bms1 |
A |
T |
6: 118,381,544 (GRCm39) |
S665T |
probably benign |
Het |
| Ccser1 |
A |
T |
6: 62,357,126 (GRCm39) |
T855S |
possibly damaging |
Het |
| Cfap36 |
C |
T |
11: 29,172,875 (GRCm39) |
V217M |
probably benign |
Het |
| Clca3b |
T |
C |
3: 144,542,393 (GRCm39) |
N470D |
probably damaging |
Het |
| Cort |
A |
G |
4: 149,209,752 (GRCm39) |
F100S |
probably damaging |
Het |
| Cyp4f14 |
G |
T |
17: 33,133,540 (GRCm39) |
D105E |
probably benign |
Het |
| Dnah1 |
A |
G |
14: 31,009,830 (GRCm39) |
S1913P |
probably benign |
Het |
| Fam91a1 |
A |
T |
15: 58,302,584 (GRCm39) |
H308L |
probably damaging |
Het |
| Fbn1 |
A |
C |
2: 125,166,867 (GRCm39) |
I2016M |
probably damaging |
Het |
| Fibcd1 |
T |
A |
2: 31,723,886 (GRCm39) |
Q251L |
possibly damaging |
Het |
| Flg2 |
T |
A |
3: 93,109,416 (GRCm39) |
Y481* |
probably null |
Het |
| Mapt |
C |
T |
11: 104,213,311 (GRCm39) |
S301L |
probably damaging |
Het |
| Meiob |
G |
A |
17: 25,042,603 (GRCm39) |
V144I |
probably benign |
Het |
| Muc4 |
G |
A |
16: 32,754,086 (GRCm38) |
G1321R |
probably benign |
Het |
| Myo5a |
T |
A |
9: 75,068,779 (GRCm39) |
C660* |
probably null |
Het |
| Necab3 |
G |
T |
2: 154,389,488 (GRCm39) |
|
probably benign |
Het |
| Nr2c2ap |
A |
G |
8: 70,585,279 (GRCm39) |
Y93C |
probably damaging |
Het |
| Nxpe5 |
A |
G |
5: 138,247,096 (GRCm39) |
D356G |
probably benign |
Het |
| Or10ak9 |
T |
A |
4: 118,726,484 (GRCm39) |
Y168N |
probably damaging |
Het |
| Or2w25 |
A |
T |
11: 59,504,147 (GRCm39) |
Y119F |
possibly damaging |
Het |
| Plce1 |
A |
G |
19: 38,734,232 (GRCm39) |
Q1544R |
probably damaging |
Het |
| Plppr4 |
T |
A |
3: 117,115,869 (GRCm39) |
T605S |
probably benign |
Het |
| Poglut1 |
C |
A |
16: 38,363,278 (GRCm39) |
W167L |
possibly damaging |
Het |
| Pou2f1 |
G |
T |
1: 165,729,867 (GRCm39) |
R162S |
probably damaging |
Het |
| Ptprf |
A |
G |
4: 118,080,417 (GRCm39) |
|
probably benign |
Het |
| Reln |
C |
A |
5: 22,244,563 (GRCm39) |
G805V |
possibly damaging |
Het |
| Rexo2 |
A |
G |
9: 48,385,747 (GRCm39) |
S126P |
probably damaging |
Het |
| Robo4 |
A |
G |
9: 37,322,400 (GRCm39) |
S844G |
probably damaging |
Het |
| Scn7a |
A |
G |
2: 66,513,671 (GRCm39) |
|
probably benign |
Het |
| Sdc1 |
A |
G |
12: 8,840,459 (GRCm39) |
T75A |
possibly damaging |
Het |
| Slc38a4 |
C |
T |
15: 96,917,690 (GRCm39) |
E12K |
probably benign |
Het |
| Spata31h1 |
T |
G |
10: 82,119,586 (GRCm39) |
M4475L |
probably benign |
Het |
| Tbck |
T |
C |
3: 132,448,854 (GRCm39) |
|
probably null |
Het |
| Tex2 |
A |
T |
11: 106,459,361 (GRCm39) |
V23E |
probably damaging |
Het |
| Zfp770 |
A |
G |
2: 114,026,413 (GRCm39) |
V552A |
probably benign |
Het |
| Zfyve26 |
T |
C |
12: 79,296,234 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Ly9 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
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 |
|
|
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 |
|
| Posted On |
2011-07-12 |
Incidental Mutation