Incidental Mutation 'R6076:Col9a1'
| ID |
482724 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
044237-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.121)
|
| Stock # |
R6076 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
1 |
| Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
| Type of Mutation |
start gained |
| DNA Base Change (assembly) |
A to T
at 24234457 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000085687
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000054588]
[ENSMUST00000088349]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000054588
|
| SMART Domains |
Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
| 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 benign
Transcript: ENSMUST00000088349
|
| SMART Domains |
Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147
| 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 |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.3%
- 20x: 95.2%
|
| 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: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ank3 |
G |
A |
10: 69,838,395 (GRCm39) |
R1566K |
possibly damaging |
Het |
| Atp6v0a1 |
T |
A |
11: 100,945,886 (GRCm39) |
I723N |
probably damaging |
Het |
| C530025M09Rik |
T |
C |
2: 149,672,670 (GRCm39) |
|
probably benign |
Het |
| Cdkn1a |
A |
G |
17: 29,318,332 (GRCm39) |
K149E |
probably damaging |
Het |
| Cep70 |
T |
A |
9: 99,180,558 (GRCm39) |
I571N |
probably damaging |
Het |
| Cimip4 |
T |
C |
15: 78,270,427 (GRCm39) |
R114G |
possibly damaging |
Het |
| Csde1 |
G |
A |
3: 102,948,545 (GRCm39) |
D132N |
possibly damaging |
Het |
| Dlk1 |
A |
G |
12: 109,425,895 (GRCm39) |
Q256R |
probably damaging |
Het |
| Epha6 |
A |
T |
16: 60,026,073 (GRCm39) |
D456E |
probably damaging |
Het |
| Ephx2 |
A |
G |
14: 66,330,297 (GRCm39) |
V354A |
probably damaging |
Het |
| Fpr-rs4 |
A |
G |
17: 18,242,317 (GRCm39) |
N108S |
probably damaging |
Het |
| Gimap1 |
C |
T |
6: 48,719,521 (GRCm39) |
Q116* |
probably null |
Het |
| Gm10784 |
T |
C |
13: 50,099,310 (GRCm39) |
|
noncoding transcript |
Het |
| Grid2ip |
G |
C |
5: 143,373,130 (GRCm39) |
S736T |
probably benign |
Het |
| Hic1 |
T |
C |
11: 75,058,154 (GRCm39) |
D245G |
probably damaging |
Het |
| Hpcal4 |
C |
A |
4: 123,084,514 (GRCm39) |
Q148K |
probably benign |
Het |
| Hspa14 |
C |
T |
2: 3,512,109 (GRCm39) |
S55N |
probably benign |
Het |
| Hspa1b |
G |
A |
17: 35,176,473 (GRCm39) |
T504I |
probably damaging |
Het |
| Jchain |
G |
T |
5: 88,675,631 (GRCm39) |
T3N |
probably benign |
Het |
| Kl |
C |
G |
5: 150,876,466 (GRCm39) |
F95L |
probably damaging |
Het |
| Kndc1 |
A |
G |
7: 139,481,954 (GRCm39) |
T115A |
probably damaging |
Het |
| Lrp8 |
G |
T |
4: 107,704,656 (GRCm39) |
R292L |
possibly damaging |
Het |
| Lrrc15 |
T |
A |
16: 30,091,806 (GRCm39) |
D511V |
probably benign |
Het |
| Mapk8 |
A |
G |
14: 33,112,250 (GRCm39) |
C213R |
probably damaging |
Het |
| Mcph1 |
C |
T |
8: 18,682,015 (GRCm39) |
P384L |
probably benign |
Het |
| Mrps7 |
T |
C |
11: 115,495,713 (GRCm39) |
S84P |
probably damaging |
Het |
| Nceh1 |
A |
C |
3: 27,333,344 (GRCm39) |
I147L |
probably benign |
Het |
| Noxa1 |
A |
T |
2: 24,975,821 (GRCm39) |
I409N |
probably damaging |
Het |
| Or1p1c |
T |
C |
11: 74,161,088 (GRCm39) |
I291T |
probably damaging |
Het |
| Pkd1 |
G |
A |
17: 24,800,004 (GRCm39) |
G2975R |
probably benign |
Het |
| Ppip5k1 |
T |
C |
2: 121,167,591 (GRCm39) |
D17G |
probably null |
Het |
| Prex2 |
T |
A |
1: 11,256,174 (GRCm39) |
Y1182N |
probably benign |
Het |
| Rasa2 |
T |
C |
9: 96,427,699 (GRCm39) |
N722S |
probably benign |
Het |
| Rcc1l |
A |
G |
5: 134,198,167 (GRCm39) |
V155A |
possibly damaging |
Het |
| Rest |
A |
G |
5: 77,430,821 (GRCm39) |
E1080G |
unknown |
Het |
| Sacs |
A |
T |
14: 61,441,985 (GRCm39) |
K1344* |
probably null |
Het |
| Sec16a |
C |
T |
2: 26,313,954 (GRCm39) |
E1884K |
probably damaging |
Het |
| Secisbp2 |
C |
A |
13: 51,833,813 (GRCm39) |
T651K |
probably damaging |
Het |
| Sema3e |
A |
G |
5: 14,291,100 (GRCm39) |
D620G |
probably benign |
Het |
| Slc6a17 |
A |
G |
3: 107,379,387 (GRCm39) |
S553P |
possibly damaging |
Het |
| Smpd5 |
C |
A |
15: 76,179,092 (GRCm39) |
N153K |
probably damaging |
Het |
| Ube2d4 |
T |
A |
15: 58,718,992 (GRCm39) |
|
noncoding transcript |
Het |
| Vps13c |
A |
G |
9: 67,818,884 (GRCm39) |
I1102V |
probably damaging |
Het |
| Wdr36 |
C |
A |
18: 32,979,998 (GRCm39) |
S241Y |
probably damaging |
Het |
| Wdr7 |
T |
A |
18: 63,872,348 (GRCm39) |
D427E |
probably damaging |
Het |
| Zfp945 |
G |
A |
17: 23,070,432 (GRCm39) |
P489L |
probably damaging |
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 |
|
|
IGL02192:Col9a1
|
APN |
1 |
24,261,068 (GRCm39) |
missense |
probably damaging |
1.00 |
|
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 |
|
|
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 |
|
| Predicted Primers |
|
| Posted On |
2017-07-14 |
Incidental Mutation