Incidental Mutation 'R2394:Col9a2'
ID |
247903 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col9a2
|
Ensembl Gene |
ENSMUSG00000028626 |
Gene Name |
collagen, type IX, alpha 2 |
Synonyms |
Col9a-2 |
MMRRC Submission |
040362-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R2394 (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: 97.0%
- 20x: 94.0%
|
Validation Efficiency |
100% (41/41) |
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: 36 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700020L13Rik |
A |
T |
7: 29,980,053 (GRCm39) |
|
probably benign |
Het |
Abca17 |
T |
C |
17: 24,500,190 (GRCm39) |
|
probably null |
Het |
Atxn7 |
T |
C |
14: 14,100,237 (GRCm38) |
V641A |
probably damaging |
Het |
C3 |
G |
A |
17: 57,529,303 (GRCm39) |
Q30* |
probably null |
Het |
Ccdc162 |
A |
G |
10: 41,445,894 (GRCm39) |
I426T |
probably damaging |
Het |
Cwc27 |
A |
C |
13: 104,932,942 (GRCm39) |
D253E |
probably benign |
Het |
Cyp1a1 |
T |
A |
9: 57,607,432 (GRCm39) |
V20D |
probably benign |
Het |
Dmbt1 |
T |
A |
7: 130,696,464 (GRCm39) |
Y892* |
probably null |
Het |
Dnhd1 |
T |
A |
7: 105,369,438 (GRCm39) |
Y4354N |
probably benign |
Het |
Dync2li1 |
T |
A |
17: 84,952,175 (GRCm39) |
I202K |
possibly damaging |
Het |
Dyrk1a |
T |
A |
16: 94,485,991 (GRCm39) |
V446E |
probably benign |
Het |
Efcab3 |
C |
A |
11: 104,629,121 (GRCm39) |
T933K |
probably benign |
Het |
Fam186b |
T |
C |
15: 99,178,058 (GRCm39) |
I423V |
probably benign |
Het |
Gm5108 |
T |
C |
5: 68,132,475 (GRCm39) |
|
probably benign |
Het |
Htr3a |
A |
G |
9: 48,817,643 (GRCm39) |
V110A |
probably benign |
Het |
Itsn2 |
C |
A |
12: 4,757,005 (GRCm39) |
S1365Y |
possibly damaging |
Het |
Lrrc46 |
T |
C |
11: 96,929,657 (GRCm39) |
I60V |
probably damaging |
Het |
Mtrex |
A |
T |
13: 113,019,702 (GRCm39) |
Y803N |
probably benign |
Het |
Nlrp14 |
T |
C |
7: 106,797,031 (GRCm39) |
V307A |
probably benign |
Het |
Nt5c2 |
A |
G |
19: 46,878,506 (GRCm39) |
|
probably null |
Het |
Obox2 |
C |
T |
7: 15,130,935 (GRCm39) |
P56S |
possibly damaging |
Het |
Olfml2b |
A |
G |
1: 170,477,319 (GRCm39) |
I151M |
possibly damaging |
Het |
Oog3 |
T |
A |
4: 143,885,884 (GRCm39) |
D238V |
probably benign |
Het |
Pde11a |
T |
C |
2: 75,889,405 (GRCm39) |
T690A |
probably benign |
Het |
Ppa1 |
A |
G |
10: 61,508,163 (GRCm39) |
|
probably benign |
Het |
Ppfia2 |
A |
G |
10: 106,655,351 (GRCm39) |
E306G |
probably damaging |
Het |
Ppic |
G |
A |
18: 53,544,119 (GRCm39) |
R89C |
probably damaging |
Het |
Ptprk |
T |
G |
10: 28,427,713 (GRCm39) |
I764S |
probably damaging |
Het |
Ripk2 |
T |
C |
4: 16,132,774 (GRCm39) |
|
probably benign |
Het |
Rnf123 |
A |
G |
9: 107,940,735 (GRCm39) |
M702T |
probably benign |
Het |
Slco1b2 |
T |
C |
6: 141,615,100 (GRCm39) |
I335T |
probably damaging |
Het |
Ssbp1 |
T |
A |
6: 40,453,743 (GRCm39) |
D96E |
probably benign |
Het |
Tpp2 |
T |
A |
1: 44,022,346 (GRCm39) |
S915T |
possibly damaging |
Het |
Unc5c |
A |
T |
3: 141,383,892 (GRCm39) |
Q90L |
probably damaging |
Het |
Vmn2r57 |
A |
G |
7: 41,049,619 (GRCm39) |
I710T |
possibly damaging |
Het |
Wdr90 |
G |
A |
17: 26,070,429 (GRCm39) |
P1104L |
probably damaging |
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 |
R2393: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'- ACAGAACCTCCCAAATCTTATCTGG -3'
(R):5'- TCAAGAGTCCCAACTGCCAG -3'
Sequencing Primer
(F):5'- AACCTCCCAAATCTTATCTGGATCTC -3'
(R):5'- AGAGACACCTCCAGCTTGG -3'
|
Posted On |
2014-11-11 |