Incidental Mutation 'R5564:Col9a1'
| ID |
436721 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
043121-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.121)
|
| Stock # |
R5564 (G1)
|
| Quality Score |
177 |
|
Status
|
Not validated
|
| Chromosome |
1 |
| Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
| Type of Mutation |
start gained |
| DNA Base Change (assembly) |
A to T
at 24234436 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: 99.7%
- 10x: 98.7%
- 20x: 96.5%
|
| Validation Efficiency |
98% (57/58) |
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aadacl2fm2 |
T |
C |
3: 59,659,513 (GRCm39) |
V322A |
probably benign |
Het |
| Abca8b |
G |
T |
11: 109,825,407 (GRCm39) |
L1598M |
probably benign |
Het |
| Adam4 |
T |
C |
12: 81,466,348 (GRCm39) |
T758A |
probably benign |
Het |
| B3galnt2 |
T |
C |
13: 14,169,814 (GRCm39) |
I424T |
probably damaging |
Het |
| Cacna1g |
T |
C |
11: 94,321,312 (GRCm39) |
Y1316C |
probably damaging |
Het |
| Cacna2d1 |
T |
C |
5: 16,517,517 (GRCm39) |
S388P |
probably damaging |
Het |
| Ccdc157 |
A |
G |
11: 4,098,765 (GRCm39) |
L247S |
probably damaging |
Het |
| Cdh8 |
A |
G |
8: 99,757,498 (GRCm39) |
I700T |
possibly damaging |
Het |
| Cdhr3 |
G |
T |
12: 33,098,985 (GRCm39) |
Y535* |
probably null |
Het |
| Clasp2 |
T |
C |
9: 113,641,836 (GRCm39) |
|
probably null |
Het |
| Col16a1 |
T |
A |
4: 129,947,151 (GRCm39) |
D165E |
probably damaging |
Het |
| Cpa3 |
A |
T |
3: 20,296,307 (GRCm39) |
I10N |
possibly damaging |
Het |
| Cstf3 |
T |
A |
2: 104,439,347 (GRCm39) |
|
probably benign |
Het |
| Dnah3 |
C |
A |
7: 119,570,689 (GRCm39) |
|
probably null |
Het |
| E2f6 |
T |
C |
12: 16,874,706 (GRCm39) |
C263R |
probably benign |
Het |
| Eps8l2 |
C |
A |
7: 140,936,534 (GRCm39) |
Q288K |
possibly damaging |
Het |
| Fam193a |
T |
A |
5: 34,578,199 (GRCm39) |
V231D |
probably damaging |
Het |
| Gjd3 |
C |
T |
11: 102,691,029 (GRCm39) |
G325S |
probably benign |
Het |
| Gpatch8 |
T |
A |
11: 102,429,111 (GRCm39) |
E39D |
unknown |
Het |
| Gpr107 |
C |
T |
2: 31,042,375 (GRCm39) |
A2V |
probably damaging |
Het |
| Kansl3 |
G |
T |
1: 36,385,045 (GRCm39) |
H629N |
possibly damaging |
Het |
| Kcna10 |
C |
A |
3: 107,101,545 (GRCm39) |
H59N |
probably benign |
Het |
| Kitl |
A |
T |
10: 99,915,886 (GRCm39) |
E138D |
possibly damaging |
Het |
| Kpna2 |
T |
C |
11: 106,881,571 (GRCm39) |
K353R |
probably damaging |
Het |
| M1ap |
T |
A |
6: 82,958,798 (GRCm39) |
I143N |
probably damaging |
Het |
| Macf1 |
A |
G |
4: 123,420,538 (GRCm39) |
S239P |
possibly damaging |
Het |
| Med13l |
T |
A |
5: 118,880,105 (GRCm39) |
S1066T |
probably damaging |
Het |
| Mettl23 |
G |
T |
11: 116,739,865 (GRCm39) |
E47* |
probably null |
Het |
| Or52i2 |
T |
C |
7: 102,319,433 (GRCm39) |
F102S |
probably damaging |
Het |
| Or5af1 |
C |
T |
11: 58,722,039 (GRCm39) |
Q20* |
probably null |
Het |
| Proca1 |
T |
A |
11: 78,092,699 (GRCm39) |
D48E |
possibly damaging |
Het |
| Rab34 |
T |
G |
11: 78,082,458 (GRCm39) |
V227G |
probably damaging |
Het |
| Rab7 |
A |
T |
6: 87,990,632 (GRCm39) |
L14Q |
probably damaging |
Het |
| Rasgef1c |
C |
T |
11: 49,847,934 (GRCm39) |
S23F |
probably benign |
Het |
| Rit1 |
A |
G |
3: 88,633,457 (GRCm39) |
|
probably benign |
Het |
| Scin |
T |
C |
12: 40,174,568 (GRCm39) |
T172A |
probably benign |
Het |
| Scmh1 |
C |
A |
4: 120,325,575 (GRCm39) |
N97K |
probably damaging |
Het |
| Skint6 |
T |
C |
4: 112,846,162 (GRCm39) |
E655G |
possibly damaging |
Het |
| Slc22a15 |
A |
G |
3: 101,771,905 (GRCm39) |
V243A |
probably benign |
Het |
| Smg1 |
A |
G |
7: 117,789,042 (GRCm39) |
|
probably benign |
Het |
| Smim7 |
C |
T |
8: 73,324,867 (GRCm39) |
G3R |
probably damaging |
Het |
| Snurf |
C |
T |
7: 59,645,282 (GRCm39) |
R44H |
possibly damaging |
Het |
| Snx13 |
G |
A |
12: 35,174,471 (GRCm39) |
A667T |
possibly damaging |
Het |
| Sowaha |
T |
G |
11: 53,369,590 (GRCm39) |
H382P |
probably damaging |
Het |
| Tbc1d2 |
C |
T |
4: 46,629,912 (GRCm39) |
G252R |
probably benign |
Het |
| Tmem259 |
G |
T |
10: 79,814,442 (GRCm39) |
|
probably null |
Het |
| Topbp1 |
A |
G |
9: 103,211,277 (GRCm39) |
T945A |
probably damaging |
Het |
| Tor1aip2 |
T |
C |
1: 155,939,307 (GRCm39) |
|
probably benign |
Het |
| Ube3b |
T |
C |
5: 114,527,136 (GRCm39) |
V118A |
probably damaging |
Het |
| Usp38 |
T |
C |
8: 81,711,717 (GRCm39) |
K773E |
probably damaging |
Het |
| Wnk1 |
G |
A |
6: 119,925,852 (GRCm39) |
|
probably benign |
Het |
| Zfp871 |
A |
G |
17: 32,994,842 (GRCm39) |
V111A |
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 |
|
|
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 |
|
| Posted On |
2016-10-24 |
Incidental Mutation