Incidental Mutation 'R2223:Col9a2'
| ID |
241604 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a2
|
| Ensembl Gene |
ENSMUSG00000028626 |
| Gene Name |
collagen, type IX, alpha 2 |
| Synonyms |
Col9a-2 |
| MMRRC Submission |
040224-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2223 (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: 98.6%
- 10x: 97.2%
- 20x: 94.8%
|
| Validation Efficiency |
100% (59/59) |
| 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 |
|---|
| Abhd18 |
A |
G |
3: 40,889,296 (GRCm39) |
|
probably benign |
Het |
| Acvr1b |
C |
T |
15: 101,100,924 (GRCm39) |
A362V |
probably benign |
Het |
| Adamts5 |
A |
C |
16: 85,696,194 (GRCm39) |
L321R |
probably damaging |
Het |
| Adamtsl1 |
A |
C |
4: 86,306,762 (GRCm39) |
D1392A |
probably benign |
Het |
| Afdn |
T |
C |
17: 14,103,999 (GRCm39) |
|
probably benign |
Het |
| Aph1b |
A |
T |
9: 66,691,921 (GRCm39) |
M121K |
probably damaging |
Het |
| Aspg |
G |
A |
12: 112,080,868 (GRCm39) |
A120T |
probably damaging |
Het |
| Atp8b1 |
T |
A |
18: 64,697,428 (GRCm39) |
N472I |
possibly damaging |
Het |
| B4galt3 |
C |
A |
1: 171,101,613 (GRCm39) |
H196N |
probably damaging |
Het |
| Cdcp3 |
A |
T |
7: 130,849,186 (GRCm39) |
|
probably null |
Het |
| Cfd |
A |
T |
10: 79,728,039 (GRCm39) |
|
probably null |
Het |
| Cntnap5b |
A |
G |
1: 100,141,412 (GRCm39) |
E242G |
probably damaging |
Het |
| Cradd |
A |
C |
10: 95,011,735 (GRCm39) |
V135G |
probably benign |
Het |
| Cry1 |
A |
G |
10: 84,979,617 (GRCm39) |
C460R |
probably damaging |
Het |
| Cryz |
A |
T |
3: 154,324,191 (GRCm39) |
N192I |
possibly damaging |
Het |
| Cyp2d11 |
T |
A |
15: 82,274,332 (GRCm39) |
M350L |
probably benign |
Het |
| Emsy |
T |
C |
7: 98,239,982 (GRCm39) |
E1091G |
possibly damaging |
Het |
| Exoc3l4 |
C |
G |
12: 111,392,586 (GRCm39) |
A471G |
possibly damaging |
Het |
| Fam184a |
G |
A |
10: 53,531,175 (GRCm39) |
T733M |
probably damaging |
Het |
| Fmo2 |
C |
T |
1: 162,725,813 (GRCm39) |
C21Y |
probably damaging |
Het |
| Glul |
T |
A |
1: 153,782,243 (GRCm39) |
|
probably null |
Het |
| Gm5174 |
T |
A |
10: 86,492,372 (GRCm39) |
|
noncoding transcript |
Het |
| Gtpbp2 |
A |
G |
17: 46,478,153 (GRCm39) |
I434V |
probably benign |
Het |
| Kctd10 |
G |
T |
5: 114,505,410 (GRCm39) |
R195S |
probably benign |
Het |
| Lrrc38 |
T |
A |
4: 143,096,419 (GRCm39) |
C243* |
probably null |
Het |
| Luc7l2 |
T |
C |
6: 38,542,659 (GRCm39) |
|
probably benign |
Het |
| Magi2 |
T |
A |
5: 20,670,670 (GRCm39) |
V111D |
probably damaging |
Het |
| Map3k5 |
T |
C |
10: 19,943,666 (GRCm39) |
V590A |
possibly damaging |
Het |
| Megf11 |
G |
A |
9: 64,567,713 (GRCm39) |
G401S |
possibly damaging |
Het |
| Mgat4d |
G |
A |
8: 84,082,301 (GRCm39) |
|
probably benign |
Het |
| Mroh1 |
T |
C |
15: 76,292,245 (GRCm39) |
|
probably null |
Het |
| Mx1 |
T |
C |
16: 97,256,432 (GRCm39) |
|
probably benign |
Het |
| Nlrp1b |
A |
G |
11: 71,046,815 (GRCm39) |
|
probably benign |
Het |
| Ntrk3 |
T |
C |
7: 77,848,600 (GRCm39) |
I759V |
probably damaging |
Het |
| Or6c210 |
T |
A |
10: 129,495,678 (GRCm39) |
M1K |
probably null |
Het |
| Pde8b |
T |
C |
13: 95,179,955 (GRCm39) |
N318S |
probably damaging |
Het |
| Pkd1l1 |
T |
C |
11: 8,839,063 (GRCm39) |
T874A |
probably benign |
Het |
| Pkd1l1 |
T |
C |
11: 8,900,422 (GRCm39) |
T40A |
probably benign |
Het |
| Prdm2 |
T |
C |
4: 142,861,469 (GRCm39) |
N607S |
possibly damaging |
Het |
| Ptprn |
A |
T |
1: 75,234,581 (GRCm39) |
|
probably benign |
Het |
| Setx |
T |
G |
2: 29,038,549 (GRCm39) |
I1678S |
possibly damaging |
Het |
| Setx |
GTGGCT |
GT |
2: 29,044,073 (GRCm39) |
1814 |
probably null |
Het |
| Snap91 |
T |
C |
9: 86,674,580 (GRCm39) |
T544A |
possibly damaging |
Het |
| Sp8 |
G |
A |
12: 118,813,473 (GRCm39) |
G443S |
probably damaging |
Het |
| Stk39 |
C |
T |
2: 68,144,923 (GRCm39) |
G384S |
probably damaging |
Het |
| Sva |
T |
A |
6: 42,015,357 (GRCm39) |
M1K |
probably null |
Het |
| Trip10 |
A |
G |
17: 57,570,039 (GRCm39) |
D568G |
possibly damaging |
Het |
| Trpa1 |
A |
T |
1: 14,973,480 (GRCm39) |
F279L |
probably null |
Het |
| Ttc39b |
T |
C |
4: 83,150,999 (GRCm39) |
N532S |
probably benign |
Het |
| Ube2w |
A |
G |
1: 16,668,183 (GRCm39) |
S97P |
possibly damaging |
Het |
| Uvssa |
C |
T |
5: 33,549,407 (GRCm39) |
T356I |
probably damaging |
Het |
| Vmn1r25 |
A |
C |
6: 57,956,223 (GRCm39) |
L22R |
probably damaging |
Het |
| Vmn2r112 |
T |
G |
17: 22,820,214 (GRCm39) |
M29R |
possibly damaging |
Het |
| Vmn2r71 |
T |
A |
7: 85,273,301 (GRCm39) |
M705K |
probably benign |
Het |
| Zfp516 |
C |
A |
18: 82,973,895 (GRCm39) |
A31D |
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 |
|
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 |
|
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'- AGCTTGGTACATAGTAAATGCCAG -3'
(R):5'- AATGCCAGGCTTCCACAAAG -3'
Sequencing Primer
(F):5'- GCCAGTTATGTATTGGACAATTTCC -3'
(R):5'- GAAAGCCCAGATGCCCATGG -3'
|
| Posted On |
2014-10-15 |
Incidental Mutation