Incidental Mutation 'R9534:Col9a1'
| ID |
719591 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.092)
|
| Stock # |
R9534 (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 24224250 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Glutamic Acid
at position 144
(V144E)
|
| 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: V144E
|
| SMART Domains |
Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: V144E
| 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: 99.7%
- 20x: 99.0%
|
| 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: 41 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Actn3 |
C |
A |
19: 4,913,477 (GRCm39) |
Q651H |
probably benign |
Het |
| Ahnak |
G |
T |
19: 8,980,976 (GRCm39) |
M753I |
probably benign |
Het |
| Ap1ar |
T |
C |
3: 127,602,364 (GRCm39) |
T225A |
probably damaging |
Het |
| Asic1 |
T |
G |
15: 99,594,397 (GRCm39) |
I281S |
probably benign |
Het |
| Bard1 |
C |
T |
1: 71,114,189 (GRCm39) |
C264Y |
probably benign |
Het |
| Bltp1 |
A |
G |
3: 37,052,419 (GRCm39) |
T3040A |
probably benign |
Het |
| Bnip3l |
G |
A |
14: 67,246,214 (GRCm39) |
P7L |
possibly damaging |
Het |
| Cacna1e |
T |
C |
1: 154,320,693 (GRCm39) |
H1354R |
possibly damaging |
Het |
| Cc2d2b |
G |
T |
19: 40,799,068 (GRCm39) |
E860* |
probably null |
Het |
| Cenpn |
T |
A |
8: 117,661,474 (GRCm39) |
L191* |
probably null |
Het |
| Cep68 |
T |
C |
11: 20,190,686 (GRCm39) |
R109G |
probably benign |
Het |
| Coro2a |
T |
C |
4: 46,548,884 (GRCm39) |
T137A |
probably benign |
Het |
| Ecpas |
A |
G |
4: 58,807,867 (GRCm39) |
V1667A |
probably benign |
Het |
| Eml6 |
T |
C |
11: 29,734,155 (GRCm39) |
D1195G |
possibly damaging |
Het |
| Hspg2 |
G |
A |
4: 137,268,072 (GRCm39) |
V2130I |
probably benign |
Het |
| Ifi214 |
A |
T |
1: 173,354,092 (GRCm39) |
S193T |
probably benign |
Het |
| Iqsec3 |
C |
A |
6: 121,367,077 (GRCm39) |
V724L |
possibly damaging |
Het |
| Lamb2 |
G |
T |
9: 108,365,830 (GRCm39) |
G1445W |
probably damaging |
Het |
| Mis18bp1 |
A |
T |
12: 65,205,234 (GRCm39) |
S313T |
possibly damaging |
Het |
| Or1f19 |
A |
T |
16: 3,410,937 (GRCm39) |
I226F |
probably benign |
Het |
| Or4a68 |
A |
C |
2: 89,269,999 (GRCm39) |
V208G |
probably benign |
Het |
| Or5b104 |
T |
C |
19: 13,072,121 (GRCm39) |
E124G |
probably damaging |
Het |
| Pcdh9 |
C |
T |
14: 94,123,656 (GRCm39) |
C838Y |
probably damaging |
Het |
| Pdcd11 |
A |
G |
19: 47,108,718 (GRCm39) |
M1245V |
probably benign |
Het |
| Ppp3r1 |
A |
G |
11: 17,132,123 (GRCm39) |
Y7C |
probably benign |
Het |
| Rdx |
C |
T |
9: 51,984,482 (GRCm39) |
R330* |
probably null |
Het |
| Scaf11 |
T |
G |
15: 96,318,209 (GRCm39) |
N452H |
possibly damaging |
Het |
| Scube1 |
A |
G |
15: 83,606,102 (GRCm39) |
Y57H |
probably damaging |
Het |
| Slc35d3 |
T |
C |
10: 19,725,116 (GRCm39) |
T247A |
probably damaging |
Het |
| Slfn5 |
A |
T |
11: 82,849,523 (GRCm39) |
M341L |
probably benign |
Het |
| Smc2 |
T |
A |
4: 52,462,870 (GRCm39) |
M620K |
probably damaging |
Het |
| Smg5 |
T |
A |
3: 88,252,759 (GRCm39) |
S182T |
probably benign |
Het |
| Tdrd6 |
G |
T |
17: 43,936,510 (GRCm39) |
L1513I |
probably benign |
Het |
| Tet2 |
A |
T |
3: 133,173,689 (GRCm39) |
Y1524* |
probably null |
Het |
| Tex15 |
A |
G |
8: 34,060,999 (GRCm39) |
N143S |
probably benign |
Het |
| Urb1 |
A |
G |
16: 90,583,096 (GRCm39) |
I591T |
possibly damaging |
Het |
| Usp21 |
A |
G |
1: 171,110,942 (GRCm39) |
S435P |
probably benign |
Het |
| Usp24 |
T |
C |
4: 106,264,312 (GRCm39) |
Y1748H |
probably damaging |
Het |
| Vmn2r54 |
C |
A |
7: 12,366,093 (GRCm39) |
K280N |
probably benign |
Het |
| Zan |
G |
T |
5: 137,407,945 (GRCm39) |
C3616* |
probably null |
Het |
| Zfp804b |
T |
C |
5: 6,819,115 (GRCm39) |
D1316G |
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 |
|
|
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 |
|
|
Z1176:Col9a1
|
UTSW |
1 |
24,253,669 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- ACACTGTAGCCTTTCCGCAG -3'
(R):5'- GGTAAAGATTCGATCCTGATGCAG -3'
Sequencing Primer
(F):5'- AGCACACACACAGAAAAATGG -3'
(R):5'- GTCAATAAAAAGAGTGGCGCTTGTTC -3'
|
| Posted On |
2022-07-18 |
Incidental Mutation