Incidental Mutation 'R9414:Ly9'
| ID |
711919 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ly9
|
| Ensembl Gene |
ENSMUSG00000004707 |
| Gene Name |
lymphocyte antigen 9 |
| Synonyms |
T100, Lgp100, CD229, SLAMF3 |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R9414 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
171416172-171434917 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 171427275 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 427
(T427A)
|
| 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: T317A
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: T317A
| 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: T427A
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: T427A
| 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: T427A
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: T427A
| 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: 99.4%
- 20x: 97.7%
|
| 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: 62 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca9 |
A |
T |
11: 110,035,100 (GRCm39) |
I689K |
probably damaging |
Het |
| Agtpbp1 |
G |
T |
13: 59,609,902 (GRCm39) |
T1076K |
probably damaging |
Het |
| Ammecr1l |
A |
G |
18: 31,904,962 (GRCm39) |
T68A |
probably benign |
Het |
| Arvcf |
A |
G |
16: 18,215,580 (GRCm39) |
E264G |
probably damaging |
Het |
| Cacna1b |
C |
T |
2: 24,538,514 (GRCm39) |
D1542N |
probably damaging |
Het |
| Cacna2d2 |
A |
G |
9: 107,392,395 (GRCm39) |
T512A |
probably damaging |
Het |
| Crebbp |
A |
G |
16: 3,925,356 (GRCm39) |
C1213R |
probably damaging |
Het |
| Cybrd1 |
G |
T |
2: 70,948,567 (GRCm39) |
R35L |
probably damaging |
Het |
| Dcaf1 |
G |
A |
9: 106,757,158 (GRCm39) |
W1412* |
probably null |
Het |
| Eif4e |
T |
A |
3: 138,253,495 (GRCm39) |
D67E |
probably benign |
Het |
| Epb41 |
G |
A |
4: 131,702,162 (GRCm39) |
T491I |
probably damaging |
Het |
| Fez1 |
G |
A |
9: 36,779,247 (GRCm39) |
S308N |
probably benign |
Het |
| Fgfr3 |
A |
G |
5: 33,887,298 (GRCm39) |
S206G |
possibly damaging |
Het |
| Flcn |
A |
T |
11: 59,684,998 (GRCm39) |
N484K |
possibly damaging |
Het |
| Gdap2 |
T |
C |
3: 100,090,071 (GRCm39) |
|
probably null |
Het |
| Gfpt1 |
T |
A |
6: 87,062,265 (GRCm39) |
D541E |
probably benign |
Het |
| Gm5089 |
A |
G |
14: 122,673,604 (GRCm39) |
F39S |
unknown |
Het |
| Gm7694 |
C |
T |
1: 170,130,173 (GRCm39) |
G75D |
probably benign |
Het |
| Gpr15 |
A |
G |
16: 58,538,516 (GRCm39) |
L191S |
probably benign |
Het |
| Hmcn1 |
T |
G |
1: 150,545,187 (GRCm39) |
T2807P |
probably damaging |
Het |
| Iqgap2 |
T |
C |
13: 95,783,349 (GRCm39) |
T1276A |
|
Het |
| Itgae |
G |
T |
11: 73,002,629 (GRCm39) |
A129S |
possibly damaging |
Het |
| Kcns1 |
T |
C |
2: 164,010,378 (GRCm39) |
E127G |
probably damaging |
Het |
| Kmt2b |
T |
C |
7: 30,282,307 (GRCm39) |
E1118G |
probably damaging |
Het |
| Lair1 |
T |
C |
7: 4,013,819 (GRCm39) |
I143V |
probably benign |
Het |
| Lcmt2 |
T |
C |
2: 120,970,621 (GRCm39) |
D154G |
possibly damaging |
Het |
| Man2c1 |
A |
G |
9: 57,044,030 (GRCm39) |
T281A |
possibly damaging |
Het |
| Map4k2 |
T |
C |
19: 6,394,515 (GRCm39) |
F332L |
probably benign |
Het |
| Meak7 |
A |
T |
8: 120,495,081 (GRCm39) |
S226T |
probably benign |
Het |
| Mmp10 |
A |
T |
9: 7,502,489 (GRCm39) |
D32V |
probably benign |
Het |
| Mroh2a |
C |
T |
1: 88,179,096 (GRCm39) |
R1110W |
probably benign |
Het |
| Naip2 |
T |
A |
13: 100,298,243 (GRCm39) |
S598C |
probably damaging |
Het |
| Npnt |
T |
C |
3: 132,612,116 (GRCm39) |
N300S |
probably benign |
Het |
| Or13a20 |
C |
A |
7: 140,232,263 (GRCm39) |
R124S |
probably damaging |
Het |
| Or5b95 |
T |
C |
19: 12,657,712 (GRCm39) |
V80A |
probably benign |
Het |
| Or5k15 |
G |
A |
16: 58,710,565 (GRCm39) |
T6I |
probably benign |
Het |
| Pacsin1 |
T |
C |
17: 27,926,985 (GRCm39) |
V387A |
probably damaging |
Het |
| Pald1 |
G |
T |
10: 61,178,932 (GRCm39) |
A489E |
probably benign |
Het |
| Pcnx1 |
G |
T |
12: 81,964,978 (GRCm39) |
G382W |
probably damaging |
Het |
| Pde6b |
T |
A |
5: 108,567,592 (GRCm39) |
M294K |
possibly damaging |
Het |
| Phf20 |
T |
C |
2: 156,136,167 (GRCm39) |
V662A |
probably benign |
Het |
| Plcg1 |
T |
C |
2: 160,603,276 (GRCm39) |
I1149T |
possibly damaging |
Het |
| Prdx2 |
T |
C |
8: 85,697,196 (GRCm39) |
S79P |
probably damaging |
Het |
| Rab19 |
T |
C |
6: 39,360,855 (GRCm39) |
M1T |
probably null |
Het |
| Retn |
T |
G |
8: 3,706,908 (GRCm39) |
F44C |
probably damaging |
Het |
| Rp1 |
A |
T |
1: 4,313,841 (GRCm39) |
W507R |
unknown |
Het |
| Rsf1 |
A |
C |
7: 97,313,765 (GRCm39) |
|
probably null |
Het |
| Ryr3 |
C |
T |
2: 112,501,011 (GRCm39) |
E3561K |
possibly damaging |
Het |
| Scaf1 |
T |
A |
7: 44,652,716 (GRCm39) |
Y1220F |
unknown |
Het |
| Sowahc |
A |
G |
10: 59,058,491 (GRCm39) |
K209R |
probably benign |
Het |
| Supt20 |
T |
A |
3: 54,610,504 (GRCm39) |
I103N |
probably damaging |
Het |
| Tenm4 |
A |
G |
7: 96,545,367 (GRCm39) |
E2498G |
probably benign |
Het |
| Tet1 |
T |
C |
10: 62,674,935 (GRCm39) |
N1047S |
probably benign |
Het |
| Thap1 |
CAGCATCTGCTCGGAGCA |
CAGCA |
8: 26,650,884 (GRCm39) |
|
probably null |
Het |
| Tub |
T |
A |
7: 108,626,265 (GRCm39) |
I267N |
probably damaging |
Het |
| Uggt1 |
T |
C |
1: 36,223,507 (GRCm39) |
E594G |
probably benign |
Het |
| Vmn2r104 |
T |
A |
17: 20,250,250 (GRCm39) |
I674F |
probably damaging |
Het |
| Zbed6 |
T |
C |
1: 133,585,015 (GRCm39) |
D774G |
probably damaging |
Het |
| Zcchc4 |
T |
C |
5: 52,953,964 (GRCm39) |
S215P |
probably benign |
Het |
| Zfc3h1 |
T |
G |
10: 115,249,916 (GRCm39) |
S1177A |
possibly damaging |
Het |
| Zfp646 |
G |
A |
7: 127,481,050 (GRCm39) |
A1076T |
probably damaging |
Het |
| Zfp735 |
T |
A |
11: 73,602,023 (GRCm39) |
Y322* |
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 |
|
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 |
|
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'- TCTGGATCCCATTGCACTGAAATG -3'
(R):5'- GTCCTGTGCACATGATGAACG -3'
Sequencing Primer
(F):5'- GATCCCATTGCACTGAAATGATGCTC -3'
(R):5'- TGCACATGATGAACGGAATCTGC -3'
|
| Posted On |
2022-05-16 |
Incidental Mutation