Incidental Mutation 'IGL02192:Col9a1'
| ID |
283920 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.092)
|
| Stock # |
IGL02192
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
1 |
| Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 24261068 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Proline to Serine
at position 311
(P311S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000085687
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000054588]
[ENSMUST00000088349]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000054588
AA Change: P552S
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: P552S
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
TSPN
|
50 |
244 |
5.73e-78 |
SMART |
|
Pfam:Collagen
|
266 |
326 |
2e-11 |
PFAM |
|
Pfam:Collagen
|
308 |
358 |
3.5e-9 |
PFAM |
|
Pfam:Collagen
|
357 |
409 |
1.2e-8 |
PFAM |
|
Pfam:Collagen
|
415 |
472 |
7.8e-11 |
PFAM |
|
Pfam:Collagen
|
454 |
515 |
2.9e-11 |
PFAM |
|
Pfam:Collagen
|
592 |
667 |
3.9e-8 |
PFAM |
|
Pfam:Collagen
|
646 |
716 |
1.7e-9 |
PFAM |
|
Pfam:Collagen
|
697 |
760 |
1.6e-10 |
PFAM |
|
Pfam:Collagen
|
785 |
848 |
3.1e-11 |
PFAM |
|
low complexity region
|
878 |
899 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000088349
AA Change: P311S
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147
AA Change: P311S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
7 |
22 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
24 |
85 |
1.5e-11 |
PFAM |
|
Pfam:Collagen
|
66 |
117 |
2.7e-9 |
PFAM |
|
Pfam:Collagen
|
115 |
168 |
2.8e-8 |
PFAM |
|
Pfam:Collagen
|
174 |
231 |
5.5e-11 |
PFAM |
|
Pfam:Collagen
|
213 |
274 |
1.9e-11 |
PFAM |
|
low complexity region
|
353 |
391 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
405 |
479 |
1.3e-9 |
PFAM |
|
Pfam:Collagen
|
456 |
519 |
1e-10 |
PFAM |
|
Pfam:Collagen
|
544 |
607 |
2.4e-11 |
PFAM |
|
low complexity region
|
637 |
658 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124600
|
| Coding Region Coverage |
|
| Validation Efficiency |
|
| 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, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted mutation show no conspicuous skeletal abnormalities at birth but develop early-onset degenerative joint disease resembling osteoarthritis as well as progressive hearing loss; restoration and remodeling of trabecular bone is perturbed with minimal effects on cortical bone. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Actn4 |
A |
T |
7: 28,597,825 (GRCm39) |
M545K |
possibly damaging |
Het |
| Adamtsl1 |
A |
G |
4: 86,146,253 (GRCm39) |
E303G |
probably damaging |
Het |
| Anxa13 |
A |
T |
15: 58,220,628 (GRCm39) |
|
noncoding transcript |
Het |
| Ap2b1 |
C |
T |
11: 83,237,592 (GRCm39) |
T552I |
possibly damaging |
Het |
| Cars1 |
T |
C |
7: 143,125,325 (GRCm39) |
S388G |
probably damaging |
Het |
| Cdh18 |
A |
T |
15: 23,460,402 (GRCm39) |
D544V |
probably damaging |
Het |
| Chat |
T |
C |
14: 32,145,279 (GRCm39) |
R377G |
possibly damaging |
Het |
| Col14a1 |
A |
G |
15: 55,225,798 (GRCm39) |
T154A |
unknown |
Het |
| Cpsf3 |
G |
T |
12: 21,360,194 (GRCm39) |
|
probably benign |
Het |
| Cpsf3 |
G |
T |
12: 21,360,197 (GRCm39) |
|
probably null |
Het |
| Dock8 |
T |
C |
19: 25,055,569 (GRCm39) |
|
probably null |
Het |
| Eml6 |
A |
G |
11: 29,755,743 (GRCm39) |
I837T |
probably benign |
Het |
| Epb41 |
T |
C |
4: 131,657,028 (GRCm39) |
T792A |
probably damaging |
Het |
| Exph5 |
A |
T |
9: 53,287,625 (GRCm39) |
R1569* |
probably null |
Het |
| F13b |
A |
T |
1: 139,445,071 (GRCm39) |
T574S |
probably damaging |
Het |
| Fam184b |
G |
T |
5: 45,695,062 (GRCm39) |
D727E |
probably benign |
Het |
| Fhip1a |
A |
G |
3: 85,580,633 (GRCm39) |
L524P |
possibly damaging |
Het |
| Fhod3 |
T |
C |
18: 25,189,415 (GRCm39) |
L619P |
probably damaging |
Het |
| Fsd1l |
A |
G |
4: 53,647,754 (GRCm39) |
I66V |
probably benign |
Het |
| Fv1 |
A |
G |
4: 147,954,712 (GRCm39) |
D426G |
possibly damaging |
Het |
| Gm3371 |
A |
T |
14: 44,641,235 (GRCm39) |
|
probably benign |
Het |
| Hnf1a |
A |
T |
5: 115,098,177 (GRCm39) |
S142T |
probably damaging |
Het |
| Itgb3 |
A |
G |
11: 104,534,765 (GRCm39) |
I541V |
probably benign |
Het |
| Itgbl1 |
G |
T |
14: 124,081,338 (GRCm39) |
C239F |
probably damaging |
Het |
| Krt26 |
C |
T |
11: 99,224,471 (GRCm39) |
R349Q |
probably benign |
Het |
| Larp1b |
G |
T |
3: 40,921,929 (GRCm39) |
S116I |
probably benign |
Het |
| Lmtk3 |
A |
G |
7: 45,443,933 (GRCm39) |
|
probably benign |
Het |
| Mapk10 |
T |
C |
5: 103,137,513 (GRCm39) |
I235V |
probably damaging |
Het |
| Mctp1 |
C |
T |
13: 76,879,887 (GRCm39) |
|
probably benign |
Het |
| Megf8 |
G |
A |
7: 25,053,285 (GRCm39) |
D1819N |
probably damaging |
Het |
| Muc6 |
T |
C |
7: 141,217,717 (GRCm39) |
T2254A |
possibly damaging |
Het |
| Nbr1 |
T |
A |
11: 101,460,417 (GRCm39) |
S444T |
probably damaging |
Het |
| Ncor2 |
A |
T |
5: 125,101,301 (GRCm39) |
D1956E |
probably damaging |
Het |
| Ndufaf5 |
T |
C |
2: 140,030,663 (GRCm39) |
V183A |
probably benign |
Het |
| Nfasc |
G |
A |
1: 132,498,219 (GRCm39) |
T1155M |
probably damaging |
Het |
| Nol12 |
A |
G |
15: 78,821,374 (GRCm39) |
E78G |
probably damaging |
Het |
| Npy5r |
T |
A |
8: 67,133,998 (GRCm39) |
H265L |
probably benign |
Het |
| Or10j2 |
T |
A |
1: 173,098,417 (GRCm39) |
L225H |
probably damaging |
Het |
| Or8k16 |
G |
A |
2: 85,520,472 (GRCm39) |
G233D |
possibly damaging |
Het |
| Pop1 |
A |
G |
15: 34,529,217 (GRCm39) |
E749G |
probably benign |
Het |
| Ppil3 |
T |
C |
1: 58,477,547 (GRCm39) |
I66V |
probably damaging |
Het |
| Prl4a1 |
C |
A |
13: 28,202,554 (GRCm39) |
T43K |
possibly damaging |
Het |
| Prop1 |
A |
G |
11: 50,844,113 (GRCm39) |
|
probably benign |
Het |
| Qrsl1 |
A |
T |
10: 43,761,010 (GRCm39) |
I218N |
probably damaging |
Het |
| Rbm22 |
T |
A |
18: 60,697,484 (GRCm39) |
M63K |
possibly damaging |
Het |
| Rictor |
T |
C |
15: 6,815,895 (GRCm39) |
S1056P |
probably benign |
Het |
| Rps6kb2 |
T |
C |
19: 4,207,587 (GRCm39) |
T388A |
probably damaging |
Het |
| Slc7a5 |
A |
G |
8: 122,613,129 (GRCm39) |
|
probably benign |
Het |
| Sp100 |
A |
T |
1: 85,635,722 (GRCm39) |
D509V |
probably damaging |
Het |
| Spata18 |
G |
T |
5: 73,829,861 (GRCm39) |
|
probably null |
Het |
| Sspo |
C |
A |
6: 48,436,502 (GRCm39) |
T1254K |
possibly damaging |
Het |
| Stk19 |
A |
G |
17: 35,051,134 (GRCm39) |
|
probably benign |
Het |
| Taar8b |
T |
A |
10: 23,967,262 (GRCm39) |
I311F |
probably damaging |
Het |
| Themis2 |
C |
A |
4: 132,510,658 (GRCm39) |
|
probably null |
Het |
| Tll2 |
T |
C |
19: 41,074,702 (GRCm39) |
Y937C |
possibly damaging |
Het |
| Trim34a |
T |
A |
7: 103,896,939 (GRCm39) |
M1K |
probably null |
Het |
| Usp50 |
G |
A |
2: 126,619,958 (GRCm39) |
T118I |
possibly damaging |
Het |
| Vps13d |
G |
A |
4: 144,875,428 (GRCm39) |
S1693F |
probably benign |
Het |
| Vps16 |
T |
A |
2: 130,282,852 (GRCm39) |
I467N |
probably damaging |
Het |
| Zfp318 |
C |
T |
17: 46,707,736 (GRCm39) |
R265* |
probably null |
Het |
|
| Other mutations in Col9a1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00233:Col9a1
|
APN |
1 |
24,224,306 (GRCm39) |
missense |
unknown |
|
|
IGL00517:Col9a1
|
APN |
1 |
24,234,615 (GRCm39) |
intron |
probably benign |
|
|
IGL01125:Col9a1
|
APN |
1 |
24,263,726 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
IGL01505:Col9a1
|
APN |
1 |
24,224,205 (GRCm39) |
missense |
unknown |
|
|
IGL01583:Col9a1
|
APN |
1 |
24,224,225 (GRCm39) |
missense |
unknown |
|
|
IGL01627:Col9a1
|
APN |
1 |
24,218,689 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL01773:Col9a1
|
APN |
1 |
24,244,147 (GRCm39) |
missense |
probably benign |
0.17 |
|
IGL02117:Col9a1
|
APN |
1 |
24,276,574 (GRCm39) |
nonsense |
probably null |
|
|
IGL02346:Col9a1
|
APN |
1 |
24,262,690 (GRCm39) |
missense |
probably damaging |
0.96 |
|
IGL02383:Col9a1
|
APN |
1 |
24,224,339 (GRCm39) |
missense |
unknown |
|
|
IGL02453:Col9a1
|
APN |
1 |
24,218,438 (GRCm39) |
missense |
unknown |
|
|
IGL02553:Col9a1
|
APN |
1 |
24,261,018 (GRCm39) |
splice site |
probably benign |
|
|
IGL03412:Col9a1
|
APN |
1 |
24,249,508 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL03493:Col9a1
|
APN |
1 |
24,260,651 (GRCm39) |
splice site |
probably benign |
|
|
ANU74:Col9a1
|
UTSW |
1 |
24,224,409 (GRCm39) |
missense |
unknown |
|
|
R0076:Col9a1
|
UTSW |
1 |
24,276,578 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0076:Col9a1
|
UTSW |
1 |
24,276,578 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0090:Col9a1
|
UTSW |
1 |
24,262,643 (GRCm39) |
splice site |
probably null |
|
|
R0356:Col9a1
|
UTSW |
1 |
24,224,328 (GRCm39) |
nonsense |
probably null |
|
|
R0562:Col9a1
|
UTSW |
1 |
24,218,360 (GRCm39) |
splice site |
probably null |
|
|
R0584:Col9a1
|
UTSW |
1 |
24,263,571 (GRCm39) |
splice site |
probably benign |
|
|
R0708:Col9a1
|
UTSW |
1 |
24,276,342 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R1342:Col9a1
|
UTSW |
1 |
24,262,701 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1445:Col9a1
|
UTSW |
1 |
24,276,579 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1791:Col9a1
|
UTSW |
1 |
24,224,386 (GRCm39) |
missense |
unknown |
|
|
R1938:Col9a1
|
UTSW |
1 |
24,261,554 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2214:Col9a1
|
UTSW |
1 |
24,247,283 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2240:Col9a1
|
UTSW |
1 |
24,218,582 (GRCm39) |
missense |
unknown |
|
|
R3757:Col9a1
|
UTSW |
1 |
24,271,312 (GRCm39) |
critical splice donor site |
probably null |
|
|
R3891:Col9a1
|
UTSW |
1 |
24,224,517 (GRCm39) |
critical splice donor site |
probably null |
|
|
R4249:Col9a1
|
UTSW |
1 |
24,283,462 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4690:Col9a1
|
UTSW |
1 |
24,263,787 (GRCm39) |
splice site |
probably null |
|
|
R4918:Col9a1
|
UTSW |
1 |
24,276,339 (GRCm39) |
missense |
possibly damaging |
0.74 |
|
R4988:Col9a1
|
UTSW |
1 |
24,224,273 (GRCm39) |
missense |
unknown |
|
|
R5144:Col9a1
|
UTSW |
1 |
24,278,434 (GRCm39) |
missense |
probably benign |
0.08 |
|
R5327:Col9a1
|
UTSW |
1 |
24,234,620 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5511:Col9a1
|
UTSW |
1 |
24,218,619 (GRCm39) |
missense |
unknown |
|
|
R5519:Col9a1
|
UTSW |
1 |
24,269,335 (GRCm39) |
splice site |
probably null |
|
|
R5564:Col9a1
|
UTSW |
1 |
24,234,436 (GRCm39) |
start gained |
probably benign |
|
|
R6076:Col9a1
|
UTSW |
1 |
24,234,457 (GRCm39) |
start gained |
probably benign |
|
|
R6478:Col9a1
|
UTSW |
1 |
24,224,486 (GRCm39) |
missense |
unknown |
|
|
R6886:Col9a1
|
UTSW |
1 |
24,224,426 (GRCm39) |
missense |
unknown |
|
|
R7177:Col9a1
|
UTSW |
1 |
24,234,498 (GRCm39) |
missense |
unknown |
|
|
R7259:Col9a1
|
UTSW |
1 |
24,224,424 (GRCm39) |
missense |
unknown |
|
|
R7268:Col9a1
|
UTSW |
1 |
24,246,479 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R7347:Col9a1
|
UTSW |
1 |
24,218,484 (GRCm39) |
splice site |
probably null |
|
|
R7644:Col9a1
|
UTSW |
1 |
24,224,243 (GRCm39) |
missense |
unknown |
|
|
R7860:Col9a1
|
UTSW |
1 |
24,276,261 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8267:Col9a1
|
UTSW |
1 |
24,224,267 (GRCm39) |
missense |
unknown |
|
|
R8296:Col9a1
|
UTSW |
1 |
24,217,380 (GRCm39) |
missense |
unknown |
|
|
R8737:Col9a1
|
UTSW |
1 |
24,224,127 (GRCm39) |
missense |
unknown |
|
|
R8773:Col9a1
|
UTSW |
1 |
24,224,208 (GRCm39) |
missense |
unknown |
|
|
R8795:Col9a1
|
UTSW |
1 |
24,233,812 (GRCm39) |
missense |
unknown |
|
|
R8878:Col9a1
|
UTSW |
1 |
24,236,048 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8956:Col9a1
|
UTSW |
1 |
24,276,300 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8978:Col9a1
|
UTSW |
1 |
24,278,396 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9096:Col9a1
|
UTSW |
1 |
24,224,207 (GRCm39) |
missense |
unknown |
|
|
R9097:Col9a1
|
UTSW |
1 |
24,224,207 (GRCm39) |
missense |
unknown |
|
|
R9205:Col9a1
|
UTSW |
1 |
24,224,175 (GRCm39) |
missense |
unknown |
|
|
R9534:Col9a1
|
UTSW |
1 |
24,224,250 (GRCm39) |
missense |
unknown |
|
|
Z1176:Col9a1
|
UTSW |
1 |
24,253,669 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Posted On |
2015-04-16 |
Incidental Mutation