Incidental Mutation 'R6886:Col9a1'
ID |
536924 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col9a1
|
Ensembl Gene |
ENSMUSG00000026147 |
Gene Name |
collagen, type IX, alpha 1 |
Synonyms |
Col9a-1 |
MMRRC Submission |
044980-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.092)
|
Stock # |
R6886 (G1)
|
Quality Score |
225.009 |
Status
|
Not validated
|
Chromosome |
1 |
Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 24224426 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Threonine
at position 203
(S203T)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000051579
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000054588]
|
AlphaFold |
no structure available at present |
Predicted Effect |
unknown
Transcript: ENSMUST00000054588
AA Change: S203T
|
SMART Domains |
Protein: ENSMUSP00000051579 Gene: ENSMUSG00000026147 AA Change: S203T
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 |
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.3%
- 20x: 97.7%
|
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: 56 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Atp7b |
A |
T |
8: 22,518,706 (GRCm39) |
M44K |
probably benign |
Het |
Bad |
T |
C |
19: 6,928,702 (GRCm39) |
|
probably benign |
Het |
Bbs12 |
A |
G |
3: 37,373,390 (GRCm39) |
D61G |
probably damaging |
Het |
Bcr |
C |
T |
10: 74,989,769 (GRCm39) |
R722C |
probably damaging |
Het |
Carf |
C |
A |
1: 60,175,413 (GRCm39) |
|
probably null |
Het |
Ccdc181 |
A |
G |
1: 164,107,665 (GRCm39) |
E116G |
probably damaging |
Het |
Celsr1 |
A |
G |
15: 85,915,855 (GRCm39) |
V706A |
probably benign |
Het |
Ctsl |
T |
C |
13: 64,512,961 (GRCm39) |
|
probably null |
Het |
Exosc7 |
A |
T |
9: 122,965,023 (GRCm39) |
E277D |
probably benign |
Het |
Fam20b |
A |
T |
1: 156,518,081 (GRCm39) |
W238R |
probably damaging |
Het |
Fanci |
A |
T |
7: 79,070,090 (GRCm39) |
H430L |
possibly damaging |
Het |
Fstl4 |
A |
G |
11: 53,077,277 (GRCm39) |
D678G |
probably damaging |
Het |
Gm10801 |
TC |
TCGGC |
2: 98,494,151 (GRCm39) |
|
probably benign |
Het |
Gm11569 |
T |
A |
11: 99,689,247 (GRCm39) |
|
probably benign |
Het |
Igfn1 |
G |
A |
1: 135,901,198 (GRCm39) |
R306W |
probably damaging |
Het |
Il6 |
C |
T |
5: 30,223,201 (GRCm39) |
|
probably benign |
Het |
Khdc1c |
T |
C |
1: 21,439,749 (GRCm39) |
L100P |
possibly damaging |
Het |
Kif18a |
G |
A |
2: 109,127,008 (GRCm39) |
R314H |
probably damaging |
Het |
Kif26b |
A |
C |
1: 178,701,703 (GRCm39) |
K694T |
probably damaging |
Het |
Kndc1 |
A |
G |
7: 139,493,485 (GRCm39) |
T484A |
probably benign |
Het |
Lonrf1 |
T |
C |
8: 36,696,191 (GRCm39) |
|
probably null |
Het |
Man1a2 |
C |
T |
3: 100,563,387 (GRCm39) |
G169D |
probably benign |
Het |
Med6 |
G |
T |
12: 81,638,159 (GRCm39) |
D17E |
probably damaging |
Het |
Neb |
T |
C |
2: 52,110,236 (GRCm39) |
K204R |
probably damaging |
Het |
Nhlrc1 |
T |
A |
13: 47,167,252 (GRCm39) |
N335I |
possibly damaging |
Het |
Nlrp12 |
T |
C |
7: 3,289,313 (GRCm39) |
M400V |
probably benign |
Het |
Or7e173 |
G |
T |
9: 19,938,428 (GRCm39) |
H269N |
probably benign |
Het |
Or8k22 |
A |
T |
2: 86,163,408 (GRCm39) |
C97* |
probably null |
Het |
Pkhd1 |
C |
T |
1: 20,417,504 (GRCm39) |
S2549N |
probably benign |
Het |
Pramel26 |
A |
G |
4: 143,539,332 (GRCm39) |
F54L |
probably benign |
Het |
Rab4b |
A |
C |
7: 26,872,381 (GRCm39) |
L145R |
probably damaging |
Het |
Rad50 |
T |
C |
11: 53,577,011 (GRCm39) |
I526V |
probably benign |
Het |
Rel |
T |
C |
11: 23,694,304 (GRCm39) |
H309R |
probably benign |
Het |
Rnf2 |
G |
T |
1: 151,349,017 (GRCm39) |
N34K |
possibly damaging |
Het |
Serpina3m |
G |
T |
12: 104,355,386 (GRCm39) |
V18F |
possibly damaging |
Het |
Serpinb9c |
T |
C |
13: 33,334,310 (GRCm39) |
K244R |
probably benign |
Het |
Setbp1 |
T |
A |
18: 78,900,715 (GRCm39) |
Y984F |
probably damaging |
Het |
Slc12a5 |
T |
A |
2: 164,824,825 (GRCm39) |
M410K |
probably benign |
Het |
Smarca4 |
C |
T |
9: 21,570,127 (GRCm39) |
A710V |
probably damaging |
Het |
Snx19 |
C |
A |
9: 30,340,231 (GRCm39) |
D456E |
probably damaging |
Het |
Ssrp1 |
T |
A |
2: 84,870,280 (GRCm39) |
D101E |
probably benign |
Het |
Tax1bp1 |
A |
T |
6: 52,710,208 (GRCm39) |
E162D |
probably benign |
Het |
Tenm4 |
T |
A |
7: 96,446,599 (GRCm39) |
M823K |
possibly damaging |
Het |
Tesk1 |
A |
G |
4: 43,443,592 (GRCm39) |
D53G |
possibly damaging |
Het |
Tnrc6a |
T |
A |
7: 122,786,668 (GRCm39) |
S1577T |
probably benign |
Het |
Tpr |
A |
G |
1: 150,299,716 (GRCm39) |
I1270V |
probably benign |
Het |
Trp53bp2 |
T |
C |
1: 182,256,608 (GRCm39) |
|
probably null |
Het |
Ube4a |
A |
T |
9: 44,860,141 (GRCm39) |
I307N |
probably damaging |
Het |
Unc13b |
A |
G |
4: 43,170,156 (GRCm39) |
|
probably benign |
Het |
Vmn2r3 |
T |
C |
3: 64,166,927 (GRCm39) |
K735E |
probably damaging |
Het |
Vmn2r54 |
A |
G |
7: 12,366,080 (GRCm39) |
F285L |
probably benign |
Het |
Vmn2r81 |
T |
G |
10: 79,103,988 (GRCm39) |
S204A |
possibly damaging |
Het |
Washc1 |
A |
G |
17: 66,426,061 (GRCm39) |
D453G |
probably damaging |
Het |
Zfp329 |
T |
A |
7: 12,544,025 (GRCm39) |
I500L |
probably benign |
Het |
Zfp516 |
A |
G |
18: 82,975,125 (GRCm39) |
D441G |
probably benign |
Het |
Zfp644 |
T |
C |
5: 106,785,777 (GRCm39) |
T257A |
possibly 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 |
|
R6076:Col9a1
|
UTSW |
1 |
24,234,457 (GRCm39) |
start gained |
probably benign |
|
R6478:Col9a1
|
UTSW |
1 |
24,224,486 (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 |
PCR Primer
(F):5'- ACTGGAACATTTGGCAGATCCAG -3'
(R):5'- TCAAAGATGTCTTGGGCGCTC -3'
Sequencing Primer
(F):5'- TGGCAGATCCAGGATTCCG -3'
(R):5'- GCTCACCTTTAGCCATGCAGG -3'
|
Posted On |
2018-10-18 |