Incidental Mutation 'R2393:Col9a2'
| ID |
247849 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a2
|
| Ensembl Gene |
ENSMUSG00000028626 |
| Gene Name |
collagen, type IX, alpha 2 |
| Synonyms |
Col9a-2 |
| MMRRC Submission |
040361-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2393 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
120896763-120912522 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to G
at 120911455 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Glycine
at position 599
(R599G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000030372
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030372]
[ENSMUST00000058754]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000030372
AA Change: R599G
PolyPhen 2
Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000030372
Gene: ENSMUSG00000028626
AA Change: R599G
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
22 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
24 |
82 |
7.3e-12 |
PFAM |
|
Pfam:Collagen
|
59 |
115 |
2.4e-10 |
PFAM |
|
Pfam:Collagen
|
113 |
170 |
2e-8 |
PFAM |
|
Pfam:Collagen
|
176 |
236 |
8.9e-11 |
PFAM |
|
low complexity region
|
258 |
277 |
N/A |
INTRINSIC |
|
low complexity region
|
288 |
315 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
357 |
435 |
4.4e-8 |
PFAM |
|
Pfam:Collagen
|
459 |
523 |
6.1e-11 |
PFAM |
|
Pfam:Collagen
|
548 |
610 |
4.5e-11 |
PFAM |
|
low complexity region
|
639 |
661 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000058754
|
| SMART Domains |
Protein: ENSMUSP00000053900
Gene: ENSMUSG00000043207
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Peptidase_M48_N
|
41 |
225 |
2.5e-70 |
PFAM |
|
Pfam:Peptidase_M48
|
228 |
473 |
5.5e-75 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140119
|
| Meta Mutation Damage Score |
0.3183 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 94.7%
|
| Validation Efficiency |
100% (54/54) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca13 |
T |
A |
11: 9,225,057 (GRCm39) |
L512* |
probably null |
Het |
| Adam4 |
A |
T |
12: 81,467,485 (GRCm39) |
F379I |
probably benign |
Het |
| Ano6 |
C |
G |
15: 95,863,906 (GRCm39) |
|
probably benign |
Het |
| Apc2 |
A |
G |
10: 80,148,903 (GRCm39) |
E1319G |
possibly damaging |
Het |
| Arfgef3 |
A |
G |
10: 18,473,535 (GRCm39) |
V1588A |
possibly damaging |
Het |
| Arl8a |
T |
A |
1: 135,080,604 (GRCm39) |
V93E |
probably damaging |
Het |
| Arsi |
G |
A |
18: 61,049,723 (GRCm39) |
G202E |
probably benign |
Het |
| Cd200r2 |
T |
A |
16: 44,729,630 (GRCm39) |
I95N |
probably damaging |
Het |
| Cd209d |
A |
G |
8: 3,928,436 (GRCm39) |
|
probably null |
Het |
| Cep290 |
A |
G |
10: 100,397,100 (GRCm39) |
|
probably null |
Het |
| Chd2 |
G |
T |
7: 73,157,631 (GRCm39) |
D171E |
possibly damaging |
Het |
| Chrna7 |
G |
A |
7: 62,748,994 (GRCm39) |
A496V |
probably damaging |
Het |
| Colgalt1 |
C |
G |
8: 72,076,385 (GRCm39) |
T612S |
probably benign |
Het |
| Copg2 |
T |
C |
6: 30,787,893 (GRCm39) |
K602E |
probably benign |
Het |
| Crtc1 |
T |
A |
8: 70,840,808 (GRCm39) |
T473S |
probably benign |
Het |
| Ctbp2 |
A |
T |
7: 132,625,290 (GRCm39) |
|
probably null |
Het |
| Edem1 |
T |
G |
6: 108,829,504 (GRCm39) |
M541R |
probably damaging |
Het |
| Ehmt1 |
A |
C |
2: 24,696,229 (GRCm39) |
V953G |
probably damaging |
Het |
| Fabp3 |
C |
T |
4: 130,206,180 (GRCm39) |
T57I |
probably benign |
Het |
| Fgfr2 |
T |
C |
7: 129,828,968 (GRCm39) |
|
probably null |
Het |
| Focad |
A |
G |
4: 88,039,567 (GRCm39) |
D10G |
probably damaging |
Het |
| Gfus |
G |
T |
15: 75,798,200 (GRCm39) |
L191I |
probably damaging |
Het |
| Gm5901 |
G |
T |
7: 105,026,996 (GRCm39) |
V255F |
possibly damaging |
Het |
| Hsp90aa1 |
T |
C |
12: 110,659,840 (GRCm39) |
N416S |
probably damaging |
Het |
| Hspb1 |
T |
C |
5: 135,917,950 (GRCm39) |
F142L |
probably benign |
Het |
| Il17re |
C |
T |
6: 113,439,314 (GRCm39) |
H75Y |
possibly damaging |
Het |
| Kctd3 |
A |
G |
1: 188,713,568 (GRCm39) |
I389T |
probably damaging |
Het |
| Lhx6 |
T |
C |
2: 35,981,402 (GRCm39) |
D63G |
probably benign |
Het |
| Mepe |
A |
G |
5: 104,485,327 (GRCm39) |
T156A |
possibly damaging |
Het |
| Met |
A |
G |
6: 17,534,197 (GRCm39) |
Y680C |
probably damaging |
Het |
| Mrgpra3 |
T |
C |
7: 47,239,365 (GRCm39) |
Y187C |
possibly damaging |
Het |
| Mst1 |
T |
G |
9: 107,960,151 (GRCm39) |
|
probably null |
Het |
| Myh13 |
T |
A |
11: 67,231,184 (GRCm39) |
S394T |
possibly damaging |
Het |
| Nbeal1 |
T |
A |
1: 60,290,529 (GRCm39) |
V1042E |
probably damaging |
Het |
| Ndrg4 |
T |
A |
8: 96,432,839 (GRCm39) |
Y15* |
probably null |
Het |
| Neurl4 |
G |
A |
11: 69,797,900 (GRCm39) |
R720H |
probably damaging |
Het |
| Nfkbia |
A |
G |
12: 55,537,455 (GRCm39) |
|
probably benign |
Het |
| Nwd1 |
T |
A |
8: 73,389,055 (GRCm39) |
M202K |
probably benign |
Het |
| Or10d4 |
G |
T |
9: 39,580,569 (GRCm39) |
C72F |
possibly damaging |
Het |
| Or2av9 |
T |
A |
11: 58,381,546 (GRCm39) |
I12F |
probably benign |
Het |
| Pate2 |
T |
C |
9: 35,581,036 (GRCm39) |
|
probably benign |
Het |
| Pibf1 |
A |
G |
14: 99,480,368 (GRCm39) |
T715A |
probably benign |
Het |
| Pitpnm1 |
T |
C |
19: 4,160,935 (GRCm39) |
L858P |
probably benign |
Het |
| Pla2g3 |
A |
C |
11: 3,443,115 (GRCm39) |
S483R |
probably benign |
Het |
| Rad51ap2 |
T |
A |
12: 11,507,798 (GRCm39) |
D573E |
probably damaging |
Het |
| Rho |
T |
C |
6: 115,912,352 (GRCm39) |
|
probably benign |
Het |
| Rpl39l |
A |
T |
16: 9,992,328 (GRCm39) |
*52L |
probably null |
Het |
| Slco1a5 |
T |
A |
6: 142,194,501 (GRCm39) |
R381W |
possibly damaging |
Het |
| Spns3 |
T |
A |
11: 72,441,059 (GRCm39) |
|
probably benign |
Het |
| Srgap2 |
A |
G |
1: 131,259,872 (GRCm39) |
S493P |
probably benign |
Het |
| Tecpr2 |
T |
C |
12: 110,892,836 (GRCm39) |
S293P |
probably damaging |
Het |
| Ttn |
C |
T |
2: 76,583,211 (GRCm39) |
V20815M |
probably benign |
Het |
| Ushbp1 |
T |
C |
8: 71,847,132 (GRCm39) |
I167V |
probably benign |
Het |
| Wdr81 |
C |
T |
11: 75,340,231 (GRCm39) |
A1296T |
probably damaging |
Het |
| Zmym2 |
A |
G |
14: 57,158,180 (GRCm39) |
Y573C |
probably benign |
Het |
|
| Other mutations in Col9a2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01331:Col9a2
|
APN |
4 |
120,902,389 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL01978:Col9a2
|
APN |
4 |
120,901,863 (GRCm39) |
missense |
unknown |
|
|
IGL01995:Col9a2
|
APN |
4 |
120,907,607 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02162:Col9a2
|
APN |
4 |
120,911,531 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02931:Col9a2
|
APN |
4 |
120,910,389 (GRCm39) |
missense |
probably benign |
0.06 |
|
collision
|
UTSW |
4 |
120,906,913 (GRCm39) |
critical splice donor site |
probably null |
|
|
gravity_wave
|
UTSW |
4 |
120,901,216 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0208:Col9a2
|
UTSW |
4 |
120,909,485 (GRCm39) |
splice site |
probably benign |
|
|
R0426:Col9a2
|
UTSW |
4 |
120,901,857 (GRCm39) |
splice site |
probably benign |
|
|
R0512:Col9a2
|
UTSW |
4 |
120,911,504 (GRCm39) |
missense |
probably benign |
0.22 |
|
R0973:Col9a2
|
UTSW |
4 |
120,896,985 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1023:Col9a2
|
UTSW |
4 |
120,901,207 (GRCm39) |
missense |
unknown |
|
|
R1657:Col9a2
|
UTSW |
4 |
120,898,171 (GRCm39) |
missense |
unknown |
|
|
R1724:Col9a2
|
UTSW |
4 |
120,911,099 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2171:Col9a2
|
UTSW |
4 |
120,902,198 (GRCm39) |
nonsense |
probably null |
|
|
R2206:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2221:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2223:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2273:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2274:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2275:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2354:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2392:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2394:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3421:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3426:Col9a2
|
UTSW |
4 |
120,907,604 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R3710:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3821:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3838:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3839:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4067:Col9a2
|
UTSW |
4 |
120,909,586 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4298:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4299:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4595:Col9a2
|
UTSW |
4 |
120,902,352 (GRCm39) |
missense |
probably benign |
0.04 |
|
R4942:Col9a2
|
UTSW |
4 |
120,910,316 (GRCm39) |
missense |
possibly damaging |
0.73 |
|
R5120:Col9a2
|
UTSW |
4 |
120,896,969 (GRCm39) |
missense |
unknown |
|
|
R5434:Col9a2
|
UTSW |
4 |
120,898,162 (GRCm39) |
nonsense |
probably null |
|
|
R6143:Col9a2
|
UTSW |
4 |
120,911,060 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7027:Col9a2
|
UTSW |
4 |
120,901,216 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7056:Col9a2
|
UTSW |
4 |
120,906,913 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7417:Col9a2
|
UTSW |
4 |
120,911,489 (GRCm39) |
missense |
not run |
|
|
R7571:Col9a2
|
UTSW |
4 |
120,896,981 (GRCm39) |
missense |
unknown |
|
|
R9120:Col9a2
|
UTSW |
4 |
120,900,951 (GRCm39) |
splice site |
probably benign |
|
|
R9341:Col9a2
|
UTSW |
4 |
120,911,483 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9343:Col9a2
|
UTSW |
4 |
120,911,483 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9389:Col9a2
|
UTSW |
4 |
120,911,948 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9527:Col9a2
|
UTSW |
4 |
120,899,528 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9620:Col9a2
|
UTSW |
4 |
120,910,403 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9784:Col9a2
|
UTSW |
4 |
120,898,226 (GRCm39) |
missense |
unknown |
|
|
Z1176:Col9a2
|
UTSW |
4 |
120,910,994 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- AACCTCCCAAATCTTATCTGGATC -3'
(R):5'- TCAAGAGTCCCAACTGCCAG -3'
Sequencing Primer
(F):5'- ATCTGGATCTCCCTTTATCTAACCAG -3'
(R):5'- AGAGACACCTCCAGCTTGG -3'
|
| Posted On |
2014-11-11 |
Incidental Mutation