Incidental Mutation 'R7259:Col9a1'
| ID |
564449 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
045351-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.092)
|
| Stock # |
R7259 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 24224424 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 202
(E202G)
|
| 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: E202G
|
| SMART Domains |
Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: E202G
| 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 |
100% (64/64) |
| 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: 65 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adarb2 |
A |
G |
13: 8,620,288 (GRCm39) |
Y258C |
probably benign |
Het |
| Aebp2 |
A |
G |
6: 140,579,494 (GRCm39) |
S244G |
probably benign |
Het |
| Agl |
A |
T |
3: 116,578,230 (GRCm39) |
Y495N |
probably damaging |
Het |
| Arhgap33 |
A |
G |
7: 30,231,625 (GRCm39) |
V120A |
probably damaging |
Het |
| Asb14 |
C |
T |
14: 26,625,412 (GRCm39) |
H256Y |
probably benign |
Het |
| Atp2a2 |
A |
G |
5: 122,604,132 (GRCm39) |
Y434H |
probably benign |
Het |
| Atrnl1 |
C |
T |
19: 57,924,038 (GRCm39) |
R1268* |
probably null |
Het |
| AW554918 |
A |
G |
18: 25,422,906 (GRCm39) |
|
probably null |
Het |
| Canx |
A |
G |
11: 50,192,643 (GRCm39) |
W324R |
probably damaging |
Het |
| Crh |
C |
A |
3: 19,748,418 (GRCm39) |
A75S |
possibly damaging |
Het |
| Ctnnal1 |
T |
A |
4: 56,817,299 (GRCm39) |
|
probably null |
Het |
| Dmrta2 |
T |
A |
4: 109,839,104 (GRCm39) |
S284T |
possibly damaging |
Het |
| Dock1 |
T |
C |
7: 134,384,477 (GRCm39) |
V680A |
probably damaging |
Het |
| Duox2 |
G |
A |
2: 122,125,657 (GRCm39) |
R317C |
probably damaging |
Het |
| Elmod2 |
A |
G |
8: 84,048,138 (GRCm39) |
L108P |
probably damaging |
Het |
| Exoc6b |
A |
G |
6: 84,825,792 (GRCm39) |
S540P |
probably benign |
Het |
| Fsip2 |
C |
T |
2: 82,812,474 (GRCm39) |
A2931V |
possibly damaging |
Het |
| Gipc2 |
A |
T |
3: 151,833,693 (GRCm39) |
I196K |
probably damaging |
Het |
| Gli2 |
A |
G |
1: 118,764,264 (GRCm39) |
S1296P |
probably benign |
Het |
| Gm21103 |
T |
A |
14: 17,482,882 (GRCm39) |
Q173L |
probably damaging |
Het |
| Gpatch1 |
A |
T |
7: 34,986,546 (GRCm39) |
|
probably null |
Het |
| Grm8 |
G |
A |
6: 27,760,175 (GRCm39) |
T385I |
probably null |
Het |
| Gtf2f1 |
C |
A |
17: 57,311,562 (GRCm39) |
D283Y |
probably damaging |
Het |
| Hcar1 |
T |
A |
5: 124,017,275 (GRCm39) |
T139S |
possibly damaging |
Het |
| Hcrtr1 |
T |
A |
4: 130,029,611 (GRCm39) |
T157S |
possibly damaging |
Het |
| Htra2 |
T |
G |
6: 83,028,520 (GRCm39) |
Q436P |
possibly damaging |
Het |
| Igkv1-133 |
A |
G |
6: 67,702,522 (GRCm39) |
D80G |
probably benign |
Het |
| Il21 |
C |
A |
3: 37,281,803 (GRCm39) |
|
probably null |
Het |
| Inpp5f |
T |
A |
7: 128,271,681 (GRCm39) |
C359S |
probably benign |
Het |
| Itgb6 |
A |
T |
2: 60,480,355 (GRCm39) |
I327N |
probably damaging |
Het |
| Itgbl1 |
A |
T |
14: 124,081,316 (GRCm39) |
T232S |
probably damaging |
Het |
| Kif1a |
T |
A |
1: 93,001,532 (GRCm39) |
K266* |
probably null |
Het |
| Mcm10 |
C |
A |
2: 5,011,328 (GRCm39) |
E214D |
probably benign |
Het |
| Mefv |
T |
A |
16: 3,530,917 (GRCm39) |
I522F |
probably damaging |
Het |
| Naaladl2 |
T |
A |
3: 24,112,340 (GRCm39) |
I581F |
possibly damaging |
Het |
| Naip6 |
A |
T |
13: 100,440,863 (GRCm39) |
Y306N |
probably damaging |
Het |
| Opn1sw |
T |
A |
6: 29,378,911 (GRCm39) |
H247L |
probably benign |
Het |
| Or4c119 |
A |
C |
2: 88,986,854 (GRCm39) |
F222V |
probably benign |
Het |
| Or51v15-ps1 |
A |
T |
7: 103,278,966 (GRCm39) |
M67K |
probably damaging |
Het |
| Or5k1b |
T |
C |
16: 58,580,868 (GRCm39) |
T224A |
possibly damaging |
Het |
| Or6c68 |
T |
A |
10: 129,157,663 (GRCm39) |
M57K |
probably benign |
Het |
| Pbxip1 |
C |
A |
3: 89,352,940 (GRCm39) |
F195L |
probably benign |
Het |
| Pcdh12 |
A |
T |
18: 38,414,677 (GRCm39) |
F816Y |
probably benign |
Het |
| Pi4k2b |
C |
A |
5: 52,910,587 (GRCm39) |
N290K |
probably damaging |
Het |
| Pias2 |
T |
C |
18: 77,240,416 (GRCm39) |
S598P |
possibly damaging |
Het |
| Ppfia4 |
A |
G |
1: 134,240,838 (GRCm39) |
V835A |
probably damaging |
Het |
| Ptch1 |
T |
C |
13: 63,721,108 (GRCm39) |
K54E |
not run |
Het |
| Rnf213 |
A |
G |
11: 119,343,401 (GRCm39) |
I3589V |
|
Het |
| Scg2 |
T |
C |
1: 79,414,702 (GRCm39) |
Y7C |
probably benign |
Het |
| Sec16a |
A |
G |
2: 26,331,604 (GRCm39) |
V137A |
probably benign |
Het |
| Setdb1 |
G |
A |
3: 95,247,224 (GRCm39) |
T525I |
probably benign |
Het |
| Sgcg |
A |
T |
14: 61,462,666 (GRCm39) |
I227N |
probably benign |
Het |
| Slc35e4 |
A |
T |
11: 3,862,530 (GRCm39) |
|
probably null |
Het |
| Smarca2 |
C |
T |
19: 26,631,864 (GRCm39) |
Q560* |
probably null |
Het |
| Stk10 |
A |
G |
11: 32,548,497 (GRCm39) |
N355S |
probably benign |
Het |
| Supt6 |
A |
T |
11: 78,098,442 (GRCm39) |
D1716E |
probably damaging |
Het |
| Taok3 |
C |
T |
5: 117,390,608 (GRCm39) |
A523V |
probably benign |
Het |
| Tekt3 |
A |
G |
11: 62,974,592 (GRCm39) |
T304A |
possibly damaging |
Het |
| Ttc6 |
G |
T |
12: 57,622,970 (GRCm39) |
R123L |
probably benign |
Het |
| Tyw1 |
T |
A |
5: 130,296,713 (GRCm39) |
|
probably null |
Het |
| Ulk2 |
A |
G |
11: 61,672,909 (GRCm39) |
L895P |
probably damaging |
Het |
| Unc13c |
A |
T |
9: 73,424,645 (GRCm39) |
N1990K |
probably benign |
Het |
| Vmn2r111 |
T |
C |
17: 22,778,032 (GRCm39) |
N549S |
possibly damaging |
Het |
| Wipf1 |
A |
G |
2: 73,265,425 (GRCm39) |
S393P |
probably damaging |
Het |
| Yju2b |
T |
C |
8: 84,986,946 (GRCm39) |
S184G |
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 |
|
|
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'- CACTGGAACATTTGGCAGATCC -3'
(R):5'- AAAGATGTCTTGGGCGCTC -3'
Sequencing Primer
(F):5'- TGGCAGATCCAGGATTCCG -3'
(R):5'- GCTCACCTTTAGCCATGCAGG -3'
|
| Posted On |
2019-06-26 |
Incidental Mutation