Incidental Mutation 'R0584:Col9a1'
| ID |
56544 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
038774-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.092)
|
| Stock # |
R0584 (G1)
|
| Quality Score |
203 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
| Type of Mutation |
splice site |
| DNA Base Change (assembly) |
T to C
at 24263571 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
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.8%
- 10x: 97.2%
- 20x: 93.7%
|
| Validation Efficiency |
98% (47/48) |
| 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: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca7 |
T |
C |
10: 79,847,564 (GRCm39) |
S1745P |
probably damaging |
Het |
| Agfg2 |
G |
A |
5: 137,665,992 (GRCm39) |
T89I |
probably damaging |
Het |
| Agtr1a |
A |
G |
13: 30,565,017 (GRCm39) |
I27M |
probably damaging |
Het |
| Armh1 |
A |
T |
4: 117,087,047 (GRCm39) |
L206Q |
probably damaging |
Het |
| Asxl2 |
A |
T |
12: 3,546,632 (GRCm39) |
E472V |
probably damaging |
Het |
| Atp2c2 |
T |
A |
8: 120,465,157 (GRCm39) |
V313E |
probably benign |
Het |
| Casp12 |
A |
G |
9: 5,352,268 (GRCm39) |
I87V |
probably null |
Het |
| Ccl25 |
C |
T |
8: 4,404,085 (GRCm39) |
|
probably benign |
Het |
| Cyth4 |
A |
G |
15: 78,494,078 (GRCm39) |
|
probably null |
Het |
| Dnah9 |
A |
G |
11: 65,881,315 (GRCm39) |
Y2587H |
probably damaging |
Het |
| Dppa3 |
T |
C |
6: 122,606,951 (GRCm39) |
I147T |
probably benign |
Het |
| Fam120b |
T |
C |
17: 15,622,384 (GRCm39) |
S121P |
probably damaging |
Het |
| Fam209 |
C |
T |
2: 172,316,081 (GRCm39) |
T152M |
probably benign |
Het |
| Fam98a |
A |
G |
17: 75,851,772 (GRCm39) |
L103P |
probably damaging |
Het |
| Fcho1 |
T |
C |
8: 72,168,369 (GRCm39) |
Y218C |
probably damaging |
Het |
| Fitm1 |
T |
C |
14: 55,814,113 (GRCm39) |
V203A |
probably benign |
Het |
| Gcn1 |
G |
A |
5: 115,733,074 (GRCm39) |
R1037Q |
probably damaging |
Het |
| Gm11563 |
A |
G |
11: 99,549,451 (GRCm39) |
I101T |
unknown |
Het |
| Gpd1l |
A |
G |
9: 114,743,412 (GRCm39) |
F163L |
probably damaging |
Het |
| Grp |
C |
A |
18: 66,006,766 (GRCm39) |
A30E |
possibly damaging |
Het |
| H1f7 |
C |
A |
15: 98,154,958 (GRCm39) |
E64* |
probably null |
Het |
| Icosl |
T |
C |
10: 77,907,709 (GRCm39) |
Y90H |
possibly damaging |
Het |
| Itsn2 |
A |
G |
12: 4,747,180 (GRCm39) |
T1194A |
probably benign |
Het |
| Lrp6 |
A |
G |
6: 134,433,039 (GRCm39) |
S1431P |
probably damaging |
Het |
| Ltbp1 |
T |
C |
17: 75,670,467 (GRCm39) |
S1503P |
probably damaging |
Het |
| Mef2a |
G |
T |
7: 66,884,896 (GRCm39) |
S406* |
probably null |
Het |
| Myh13 |
G |
T |
11: 67,251,200 (GRCm39) |
E1360* |
probably null |
Het |
| Nop58 |
A |
G |
1: 59,745,919 (GRCm39) |
D400G |
probably benign |
Het |
| Or5p79 |
T |
C |
7: 108,221,622 (GRCm39) |
L201P |
probably benign |
Het |
| Or6c205 |
T |
C |
10: 129,086,817 (GRCm39) |
V138A |
probably benign |
Het |
| Oscp1 |
A |
G |
4: 125,977,387 (GRCm39) |
|
probably null |
Het |
| Pde9a |
A |
T |
17: 31,678,951 (GRCm39) |
Y264F |
probably damaging |
Het |
| Pkhd1 |
T |
A |
1: 20,309,660 (GRCm39) |
K2763* |
probably null |
Het |
| Prkci |
T |
A |
3: 31,079,289 (GRCm39) |
C42* |
probably null |
Het |
| Ptprr |
T |
C |
10: 116,087,063 (GRCm39) |
V270A |
probably damaging |
Het |
| Rsf1 |
T |
A |
7: 97,311,335 (GRCm39) |
N688K |
possibly damaging |
Het |
| S1pr3 |
A |
T |
13: 51,573,697 (GRCm39) |
M293L |
probably benign |
Het |
| Scn10a |
A |
C |
9: 119,499,597 (GRCm39) |
L232R |
probably damaging |
Het |
| Sirt5 |
T |
A |
13: 43,548,204 (GRCm39) |
|
probably null |
Het |
| Sp6 |
C |
T |
11: 96,913,091 (GRCm39) |
T268M |
probably damaging |
Het |
| Spag5 |
A |
G |
11: 78,194,921 (GRCm39) |
N76S |
possibly damaging |
Het |
| Tecta |
T |
C |
9: 42,259,204 (GRCm39) |
N1560D |
possibly damaging |
Het |
| Togaram1 |
T |
C |
12: 65,014,279 (GRCm39) |
L510P |
probably damaging |
Het |
| Umps |
A |
G |
16: 33,779,494 (GRCm39) |
I401T |
probably damaging |
Het |
| Vars2 |
A |
G |
17: 35,977,578 (GRCm39) |
V118A |
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 |
|
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGGCTGATGAGACTGTCTTCCTGAAA -3'
(R):5'- CCCTGTGGAAAGGAAAGCAGAGATAC -3'
Sequencing Primer
(F):5'- gccaatgccatactccgtc -3'
(R):5'- GATACAATGAGCCAACTATTCCTGG -3'
|
| Posted On |
2013-07-11 |
Incidental Mutation