Incidental Mutation 'R3821:Col9a2'
ID |
274906 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col9a2
|
Ensembl Gene |
ENSMUSG00000028626 |
Gene Name |
collagen, type IX, alpha 2 |
Synonyms |
Col9a-2 |
MMRRC Submission |
040883-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R3821 (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: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.8%
|
Validation Efficiency |
100% (67/67) |
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: 69 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Aarsd1 |
T |
A |
11: 101,301,971 (GRCm39) |
I332F |
probably damaging |
Het |
Abcd2 |
C |
T |
15: 91,058,908 (GRCm39) |
G512D |
probably damaging |
Het |
Acp3 |
G |
T |
9: 104,201,916 (GRCm39) |
Q76K |
probably damaging |
Het |
Adamtsl3 |
G |
T |
7: 82,255,687 (GRCm39) |
|
probably benign |
Het |
Alox8 |
T |
A |
11: 69,077,308 (GRCm39) |
I481F |
probably damaging |
Het |
Anp32e |
A |
T |
3: 95,842,181 (GRCm39) |
I100L |
probably benign |
Het |
Arpin |
G |
A |
7: 79,579,408 (GRCm39) |
R72C |
probably damaging |
Het |
C6 |
A |
G |
15: 4,819,066 (GRCm39) |
E466G |
probably benign |
Het |
Ccdc13 |
C |
A |
9: 121,660,085 (GRCm39) |
L76F |
probably damaging |
Het |
Cd44 |
T |
C |
2: 102,731,738 (GRCm39) |
|
probably null |
Het |
Clgn |
A |
G |
8: 84,147,106 (GRCm39) |
I353V |
probably null |
Het |
Cnot6 |
A |
T |
11: 49,579,999 (GRCm39) |
S98T |
probably benign |
Het |
Cramp1 |
G |
A |
17: 25,193,756 (GRCm39) |
T908I |
probably damaging |
Het |
Dnah9 |
C |
A |
11: 65,741,829 (GRCm39) |
|
probably null |
Het |
Ehd3 |
A |
T |
17: 74,134,390 (GRCm39) |
I250F |
probably benign |
Het |
Eml2 |
T |
C |
7: 18,936,911 (GRCm39) |
V555A |
possibly damaging |
Het |
Erbb4 |
A |
G |
1: 68,345,072 (GRCm39) |
S550P |
probably damaging |
Het |
Fchsd1 |
A |
G |
18: 38,102,510 (GRCm39) |
|
probably benign |
Het |
Flad1 |
T |
A |
3: 89,318,494 (GRCm39) |
I20F |
probably damaging |
Het |
Frem2 |
A |
T |
3: 53,559,836 (GRCm39) |
L1557Q |
probably damaging |
Het |
Gbf1 |
T |
C |
19: 46,253,246 (GRCm39) |
I506T |
probably damaging |
Het |
Gm20730 |
C |
T |
6: 43,058,656 (GRCm39) |
S52N |
probably benign |
Het |
Hoxc9 |
A |
G |
15: 102,890,596 (GRCm39) |
K171R |
probably benign |
Het |
Hscb |
A |
T |
5: 110,984,194 (GRCm39) |
D52E |
probably damaging |
Het |
Htr1b |
A |
T |
9: 81,514,487 (GRCm39) |
I40N |
probably benign |
Het |
Ido2 |
T |
C |
8: 25,023,771 (GRCm39) |
I356V |
probably benign |
Het |
Insyn2b |
T |
C |
11: 34,353,007 (GRCm39) |
S350P |
probably benign |
Het |
Irs1 |
T |
C |
1: 82,267,770 (GRCm39) |
T149A |
probably benign |
Het |
Itgam |
A |
G |
7: 127,711,458 (GRCm39) |
|
probably null |
Het |
Itpr2 |
A |
T |
6: 146,319,224 (GRCm39) |
H244Q |
probably damaging |
Het |
Kcnma1 |
A |
G |
14: 23,417,679 (GRCm39) |
I846T |
probably damaging |
Het |
Kdm3a |
A |
T |
6: 71,588,661 (GRCm39) |
D449E |
probably benign |
Het |
Lama1 |
C |
A |
17: 68,086,041 (GRCm39) |
|
probably null |
Het |
Lhfpl4 |
A |
G |
6: 113,171,069 (GRCm39) |
V39A |
probably benign |
Het |
Marf1 |
A |
T |
16: 13,960,418 (GRCm39) |
L542Q |
probably damaging |
Het |
Mns1 |
A |
G |
9: 72,346,730 (GRCm39) |
E71G |
probably damaging |
Het |
Mrc2 |
G |
A |
11: 105,239,257 (GRCm39) |
|
probably null |
Het |
Mrpl19 |
C |
A |
6: 81,938,987 (GRCm39) |
E272* |
probably null |
Het |
Ncoa6 |
T |
A |
2: 155,248,858 (GRCm39) |
N1482I |
probably damaging |
Het |
Neto2 |
C |
A |
8: 86,389,924 (GRCm39) |
E180* |
probably null |
Het |
Or2a51 |
A |
G |
6: 43,178,604 (GRCm39) |
T9A |
probably benign |
Het |
Pcdhga10 |
A |
G |
18: 37,880,995 (GRCm39) |
N252S |
probably damaging |
Het |
Pcdhgb7 |
C |
A |
18: 37,885,286 (GRCm39) |
T152K |
possibly damaging |
Het |
Ptprb |
G |
T |
10: 116,185,979 (GRCm39) |
R1678L |
probably benign |
Het |
Ptprg |
A |
T |
14: 12,226,375 (GRCm38) |
I1323L |
probably benign |
Het |
Rab40b |
T |
A |
11: 121,248,874 (GRCm39) |
N127I |
probably damaging |
Het |
Scn10a |
A |
G |
9: 119,467,699 (GRCm39) |
C814R |
probably benign |
Het |
Sdhb |
C |
T |
4: 140,706,399 (GRCm39) |
R279* |
probably null |
Het |
Shroom4 |
C |
T |
X: 6,536,276 (GRCm39) |
Q1165* |
probably null |
Het |
Slc17a4 |
C |
T |
13: 24,085,752 (GRCm39) |
R387H |
probably benign |
Het |
Slc20a2 |
A |
G |
8: 23,028,918 (GRCm39) |
I130V |
probably benign |
Het |
Slitrk3 |
T |
C |
3: 72,956,549 (GRCm39) |
Y741C |
possibly damaging |
Het |
Tas1r1 |
G |
T |
4: 152,119,138 (GRCm39) |
L144I |
probably benign |
Het |
Tenm2 |
A |
T |
11: 35,915,147 (GRCm39) |
I2129N |
probably damaging |
Het |
Tmbim1 |
A |
G |
1: 74,333,089 (GRCm39) |
V92A |
probably damaging |
Het |
Tmem131 |
T |
A |
1: 36,847,477 (GRCm39) |
H1207L |
probably damaging |
Het |
Tmem209 |
G |
T |
6: 30,505,959 (GRCm39) |
P116T |
probably damaging |
Het |
Tmem8b |
C |
A |
4: 43,689,745 (GRCm39) |
H800N |
probably damaging |
Het |
Tnfsf8 |
A |
G |
4: 63,779,127 (GRCm39) |
V57A |
probably benign |
Het |
Topaz1 |
A |
G |
9: 122,626,848 (GRCm39) |
D1492G |
possibly damaging |
Het |
Trank1 |
G |
A |
9: 111,207,887 (GRCm39) |
G1711R |
probably damaging |
Het |
Trpc6 |
A |
T |
9: 8,610,279 (GRCm39) |
D249V |
probably damaging |
Het |
Ubr3 |
G |
A |
2: 69,824,157 (GRCm39) |
|
probably null |
Het |
Ufc1 |
A |
G |
1: 171,117,172 (GRCm39) |
|
probably benign |
Het |
Unc5cl |
T |
C |
17: 48,767,001 (GRCm39) |
L125P |
possibly damaging |
Het |
Usb1 |
G |
A |
8: 96,060,061 (GRCm39) |
S57N |
probably benign |
Het |
Wdfy1 |
A |
G |
1: 79,684,017 (GRCm39) |
S373P |
probably benign |
Het |
Zfp618 |
G |
A |
4: 63,051,801 (GRCm39) |
A861T |
probably benign |
Het |
Zfp831 |
T |
C |
2: 174,485,816 (GRCm39) |
S164P |
possibly 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 |
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 |
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'- AGAACCTCCCAAATCTTATCTGGATC -3'
(R):5'- TCAAGAGTCCCAACTGCCAG -3'
Sequencing Primer
(F):5'- ATCTGGATCTCCCTTTATCTAACCAG -3'
(R):5'- AGAGACACCTCCAGCTTGG -3'
|
Posted On |
2015-04-02 |