Incidental Mutation 'R8296:Col9a1'
| ID |
638911 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
067785-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.092)
|
| Stock # |
R8296 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 24217380 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Proline to Threonine
at position 19
(P19T)
|
| 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: P19T
|
| SMART Domains |
Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: P19T
| 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: 99.6%
- 20x: 98.8%
|
| Validation Efficiency |
100% (77/77) |
| 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: 77 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2210408I21Rik |
T |
A |
13: 77,415,896 (GRCm39) |
L663Q |
probably damaging |
Het |
| 2610008E11Rik |
C |
G |
10: 78,903,568 (GRCm39) |
R249S |
probably benign |
Het |
| 6030469F06Rik |
A |
G |
12: 31,235,058 (GRCm39) |
N146S |
noncoding transcript |
Het |
| Abcb5 |
G |
A |
12: 118,838,467 (GRCm39) |
P1032S |
probably benign |
Het |
| Acvr2a |
A |
T |
2: 48,789,736 (GRCm39) |
D493V |
possibly damaging |
Het |
| Amacr |
A |
G |
15: 10,995,004 (GRCm39) |
D272G |
probably benign |
Het |
| Bach1 |
A |
C |
16: 87,526,467 (GRCm39) |
K643T |
probably damaging |
Het |
| Bmt2 |
T |
C |
6: 13,628,672 (GRCm39) |
Y337C |
probably damaging |
Het |
| Bsn |
A |
G |
9: 107,994,578 (GRCm39) |
S566P |
probably benign |
Het |
| Cass4 |
A |
C |
2: 172,269,094 (GRCm39) |
D392A |
probably benign |
Het |
| Cbx2 |
A |
G |
11: 118,918,954 (GRCm39) |
E173G |
probably damaging |
Het |
| Ccdc166 |
G |
C |
15: 75,852,860 (GRCm39) |
A369G |
probably benign |
Het |
| Ccdc77 |
G |
A |
6: 120,308,870 (GRCm39) |
T315M |
possibly damaging |
Het |
| Ceacam10 |
C |
A |
7: 24,480,513 (GRCm39) |
H215N |
unknown |
Het |
| Ces1e |
C |
T |
8: 93,929,947 (GRCm39) |
M445I |
probably benign |
Het |
| Ces2b |
T |
G |
8: 105,563,112 (GRCm39) |
V350G |
possibly damaging |
Het |
| Chtf18 |
A |
G |
17: 25,941,165 (GRCm39) |
L611P |
probably benign |
Het |
| Csf1r |
A |
T |
18: 61,250,750 (GRCm39) |
N487I |
probably damaging |
Het |
| Csl |
A |
T |
10: 99,594,161 (GRCm39) |
H301Q |
probably damaging |
Het |
| Cyp24a1 |
G |
A |
2: 170,332,036 (GRCm39) |
T330M |
probably damaging |
Het |
| Ddb2 |
T |
C |
2: 91,042,645 (GRCm39) |
D405G |
probably damaging |
Het |
| Degs1 |
A |
G |
1: 182,110,241 (GRCm39) |
F10L |
probably benign |
Het |
| Dhrs2 |
T |
A |
14: 55,477,928 (GRCm39) |
I220N |
probably damaging |
Het |
| Dlg5 |
T |
C |
14: 24,198,328 (GRCm39) |
D1535G |
possibly damaging |
Het |
| Dpy19l1 |
A |
G |
9: 24,414,372 (GRCm39) |
S19P |
probably benign |
Het |
| Eif3l |
A |
C |
15: 78,963,220 (GRCm39) |
E134A |
possibly damaging |
Het |
| Epb41 |
C |
A |
4: 131,664,772 (GRCm39) |
V90L |
|
Het |
| Flad1 |
A |
T |
3: 89,316,109 (GRCm39) |
V151D |
probably damaging |
Het |
| Gja10 |
A |
T |
4: 32,601,568 (GRCm39) |
I272N |
probably benign |
Het |
| Glmp |
T |
A |
3: 88,233,580 (GRCm39) |
D178E |
probably benign |
Het |
| Gm16494 |
G |
A |
17: 47,327,750 (GRCm39) |
P45S |
probably damaging |
Het |
| Gm4553 |
T |
C |
7: 141,719,458 (GRCm39) |
D6G |
unknown |
Het |
| Grid2 |
G |
A |
6: 63,233,929 (GRCm39) |
|
probably null |
Het |
| Icmt |
A |
G |
4: 152,387,482 (GRCm39) |
M226V |
probably benign |
Het |
| Igkv5-39 |
T |
C |
6: 69,877,607 (GRCm39) |
S50G |
probably benign |
Het |
| Ints5 |
T |
C |
19: 8,872,484 (GRCm39) |
S148P |
probably damaging |
Het |
| Itga2b |
A |
C |
11: 102,351,985 (GRCm39) |
V504G |
possibly damaging |
Het |
| Krt20 |
T |
A |
11: 99,323,063 (GRCm39) |
Y253F |
probably damaging |
Het |
| Man2a2 |
T |
A |
7: 80,018,656 (GRCm39) |
I68L |
probably damaging |
Het |
| Mpi |
G |
A |
9: 57,455,954 (GRCm39) |
T176I |
probably benign |
Het |
| Msh6 |
C |
T |
17: 88,294,340 (GRCm39) |
R1032C |
probably damaging |
Het |
| Myot |
C |
T |
18: 44,475,416 (GRCm39) |
T179I |
probably damaging |
Het |
| Neb |
A |
G |
2: 52,116,601 (GRCm39) |
S946P |
|
Het |
| Notch3 |
G |
A |
17: 32,341,713 (GRCm39) |
A2013V |
probably damaging |
Het |
| Nr1d1 |
T |
C |
11: 98,662,133 (GRCm39) |
Y167C |
probably damaging |
Het |
| Or52h7 |
T |
A |
7: 104,213,593 (GRCm39) |
F55Y |
probably benign |
Het |
| Or52n2c |
T |
C |
7: 104,574,828 (GRCm39) |
I48V |
probably benign |
Het |
| Or7g32 |
A |
G |
9: 19,408,377 (GRCm39) |
E111G |
probably damaging |
Het |
| Or8k40 |
A |
C |
2: 86,584,893 (GRCm39) |
L63R |
probably damaging |
Het |
| P4ha3 |
G |
A |
7: 99,966,309 (GRCm39) |
V485M |
probably damaging |
Het |
| Pbk |
T |
A |
14: 66,054,185 (GRCm39) |
C243* |
probably null |
Het |
| Pde4b |
T |
A |
4: 102,459,983 (GRCm39) |
L388H |
possibly damaging |
Het |
| Pecam1 |
T |
C |
11: 106,579,745 (GRCm39) |
D439G |
probably benign |
Het |
| Pknox2 |
A |
T |
9: 36,822,459 (GRCm39) |
M230K |
probably benign |
Het |
| Plekhh2 |
A |
G |
17: 84,908,113 (GRCm39) |
I1185V |
probably damaging |
Het |
| Polr3g |
A |
G |
13: 81,842,682 (GRCm39) |
V111A |
unknown |
Het |
| Prkcg |
G |
C |
7: 3,377,580 (GRCm39) |
E562D |
probably benign |
Het |
| Rftn1 |
G |
T |
17: 50,354,408 (GRCm39) |
A318D |
probably damaging |
Het |
| Rnf123 |
A |
T |
9: 107,940,089 (GRCm39) |
V768D |
probably damaging |
Het |
| Rps16 |
T |
A |
7: 28,052,008 (GRCm39) |
S129T |
probably benign |
Het |
| Scg2 |
A |
T |
1: 79,413,222 (GRCm39) |
N460K |
probably benign |
Het |
| Sct |
T |
C |
7: 140,858,807 (GRCm39) |
S42G |
probably damaging |
Het |
| Spef2 |
A |
T |
15: 9,727,629 (GRCm39) |
N151K |
probably benign |
Het |
| Syce1l |
C |
A |
8: 114,380,721 (GRCm39) |
D144E |
possibly damaging |
Het |
| Syt17 |
T |
C |
7: 118,036,069 (GRCm39) |
Y99C |
probably damaging |
Het |
| Tgfbr3 |
T |
C |
5: 107,287,640 (GRCm39) |
N520D |
probably damaging |
Het |
| Thsd7b |
A |
G |
1: 129,523,193 (GRCm39) |
S76G |
probably benign |
Het |
| Tmem63a |
G |
T |
1: 180,788,685 (GRCm39) |
V341F |
probably benign |
Het |
| Trim5 |
A |
G |
7: 103,914,993 (GRCm39) |
S359P |
probably damaging |
Het |
| Tst |
A |
T |
15: 78,284,020 (GRCm39) |
V269E |
probably damaging |
Het |
| Ubr3 |
A |
T |
2: 69,784,706 (GRCm39) |
I808F |
probably null |
Het |
| Ugt3a1 |
T |
A |
15: 9,362,024 (GRCm39) |
Y267N |
probably benign |
Het |
| Wwc1 |
A |
T |
11: 35,761,384 (GRCm39) |
|
probably benign |
Het |
| Zfp36l2 |
G |
T |
17: 84,494,552 (GRCm39) |
N28K |
probably damaging |
Het |
| Zfp57 |
A |
G |
17: 37,321,136 (GRCm39) |
D330G |
probably benign |
Het |
| Zgrf1 |
C |
A |
3: 127,377,644 (GRCm39) |
S963Y |
probably damaging |
Het |
| Zranb2 |
A |
G |
3: 157,247,412 (GRCm39) |
K197E |
unknown |
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 |
|
|
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 |
|
|
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'- TTCGCAGAGTTCCTAGGTGAG -3'
(R):5'- ACCAGCTTACAGTTGAGACTCC -3'
Sequencing Primer
(F):5'- CCTAGGTGAGCTTTCAAAATGG -3'
(R):5'- ACAGTTGAGACTCCCTTTCTAGG -3'
|
| Posted On |
2020-07-28 |
Incidental Mutation