Incidental Mutation 'R2240:Col9a1'
| ID |
240279 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
040240-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.121)
|
| Stock # |
R2240 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
1 |
| Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 24218582 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 65
(I65V)
|
| 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: I65V
|
| SMART Domains |
Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: I65V
| 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: 99.2%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.5%
|
| 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: 74 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca3 |
T |
A |
17: 24,595,417 (GRCm39) |
I318N |
probably damaging |
Het |
| Abl1 |
A |
G |
2: 31,690,517 (GRCm39) |
K679E |
probably benign |
Het |
| Actr8 |
A |
G |
14: 29,711,714 (GRCm39) |
H420R |
possibly damaging |
Het |
| Arhgap29 |
T |
A |
3: 121,805,102 (GRCm39) |
V897D |
probably benign |
Het |
| Bckdk |
C |
A |
7: 127,504,590 (GRCm39) |
R105S |
probably damaging |
Het |
| Bicc1 |
A |
G |
10: 70,782,633 (GRCm39) |
|
probably null |
Het |
| Brd4 |
T |
C |
17: 32,432,613 (GRCm39) |
|
probably benign |
Het |
| Camk2g |
T |
C |
14: 20,815,514 (GRCm39) |
E184G |
probably damaging |
Het |
| Camta1 |
T |
C |
4: 151,169,032 (GRCm39) |
S240G |
possibly damaging |
Het |
| Cbx7 |
C |
A |
15: 79,802,558 (GRCm39) |
A240S |
probably damaging |
Het |
| Ccdc181 |
A |
T |
1: 164,107,596 (GRCm39) |
D93V |
probably damaging |
Het |
| Ces2g |
A |
C |
8: 105,689,134 (GRCm39) |
S37R |
probably benign |
Het |
| Clca3a1 |
T |
A |
3: 144,714,746 (GRCm39) |
R624W |
probably damaging |
Het |
| Clca3b |
T |
C |
3: 144,531,696 (GRCm39) |
K703E |
probably benign |
Het |
| Clec2h |
T |
C |
6: 128,652,845 (GRCm39) |
V204A |
probably benign |
Het |
| Cltb |
T |
C |
13: 54,746,967 (GRCm39) |
N3S |
possibly damaging |
Het |
| D430041D05Rik |
C |
T |
2: 103,987,161 (GRCm39) |
R1895Q |
probably damaging |
Het |
| Dnah1 |
T |
C |
14: 31,021,931 (GRCm39) |
S1191G |
probably benign |
Het |
| Ehf |
G |
A |
2: 103,104,420 (GRCm39) |
P163S |
probably benign |
Het |
| Fam170b |
A |
C |
14: 32,557,825 (GRCm39) |
H220P |
probably damaging |
Het |
| Fastkd1 |
G |
A |
2: 69,527,297 (GRCm39) |
T598I |
probably benign |
Het |
| Fignl2 |
C |
T |
15: 100,951,916 (GRCm39) |
G122D |
probably damaging |
Het |
| Foxp4 |
C |
A |
17: 48,182,201 (GRCm39) |
V530L |
unknown |
Het |
| Gcnt1 |
G |
T |
19: 17,306,695 (GRCm39) |
D343E |
possibly damaging |
Het |
| Gja8 |
T |
G |
3: 96,827,618 (GRCm39) |
N15H |
probably benign |
Het |
| Gm128 |
T |
C |
3: 95,148,243 (GRCm39) |
E17G |
probably benign |
Het |
| Gnl1 |
T |
C |
17: 36,293,571 (GRCm39) |
V252A |
probably benign |
Het |
| Gpld1 |
G |
A |
13: 25,166,490 (GRCm39) |
|
probably null |
Het |
| Gpr179 |
A |
G |
11: 97,242,559 (GRCm39) |
L95P |
probably damaging |
Het |
| Gtf2a1 |
A |
T |
12: 91,553,513 (GRCm39) |
D31E |
possibly damaging |
Het |
| Il12a |
T |
A |
3: 68,601,517 (GRCm39) |
Y58* |
probably null |
Het |
| Il1r2 |
T |
C |
1: 40,144,630 (GRCm39) |
W106R |
probably damaging |
Het |
| Kif26b |
A |
G |
1: 178,543,488 (GRCm39) |
S374G |
probably benign |
Het |
| Mafb |
A |
T |
2: 160,207,947 (GRCm39) |
V217E |
probably damaging |
Het |
| Mapk13 |
T |
A |
17: 28,997,085 (GRCm39) |
D292E |
probably damaging |
Het |
| Matn2 |
A |
G |
15: 34,433,209 (GRCm39) |
D871G |
probably damaging |
Het |
| Mdn1 |
C |
A |
4: 32,765,701 (GRCm39) |
T5220K |
possibly damaging |
Het |
| Mfsd6 |
T |
C |
1: 52,699,978 (GRCm39) |
I723M |
probably damaging |
Het |
| Mia2 |
G |
A |
12: 59,154,668 (GRCm39) |
S127N |
probably benign |
Het |
| Mpeg1 |
A |
C |
19: 12,440,402 (GRCm39) |
E620A |
probably damaging |
Het |
| Mrgprb3 |
A |
T |
7: 48,293,389 (GRCm39) |
F54Y |
probably damaging |
Het |
| Mtx2 |
A |
G |
2: 74,699,696 (GRCm39) |
I156V |
probably benign |
Het |
| Neurog1 |
T |
C |
13: 56,399,348 (GRCm39) |
E133G |
probably damaging |
Het |
| Nid2 |
G |
A |
14: 19,855,982 (GRCm39) |
D1236N |
probably damaging |
Het |
| Nif3l1 |
A |
G |
1: 58,491,288 (GRCm39) |
T213A |
probably benign |
Het |
| Or7e173 |
A |
G |
9: 19,938,440 (GRCm39) |
S265P |
probably damaging |
Het |
| Otog |
A |
G |
7: 45,890,453 (GRCm39) |
M1V |
probably null |
Het |
| Pde4dip |
C |
T |
3: 97,631,480 (GRCm39) |
R1143K |
probably benign |
Het |
| Pgam2 |
T |
C |
11: 5,753,265 (GRCm39) |
|
probably benign |
Het |
| Plec |
T |
C |
15: 76,090,250 (GRCm39) |
D30G |
probably damaging |
Het |
| Pramel5 |
C |
A |
4: 143,999,506 (GRCm39) |
E194* |
probably null |
Het |
| Prss22 |
T |
A |
17: 24,215,755 (GRCm39) |
S56C |
probably damaging |
Het |
| Rab23 |
A |
G |
1: 33,778,406 (GRCm39) |
N216S |
probably benign |
Het |
| Rasgrf1 |
A |
T |
9: 89,858,815 (GRCm39) |
E491V |
probably damaging |
Het |
| Rbbp8 |
C |
T |
18: 11,810,726 (GRCm39) |
T76I |
probably damaging |
Het |
| Rtn2 |
G |
A |
7: 19,020,754 (GRCm39) |
|
probably null |
Het |
| Sdr39u1 |
A |
T |
14: 56,137,124 (GRCm39) |
N62K |
probably damaging |
Het |
| Secisbp2l |
C |
T |
2: 125,582,657 (GRCm39) |
G933D |
possibly damaging |
Het |
| Slc26a3 |
T |
C |
12: 31,507,071 (GRCm39) |
V342A |
probably damaging |
Het |
| Slc49a3 |
A |
G |
5: 108,592,573 (GRCm39) |
S234P |
probably benign |
Het |
| Snx30 |
G |
T |
4: 59,886,515 (GRCm39) |
C308F |
probably damaging |
Het |
| Timd2 |
A |
T |
11: 46,569,043 (GRCm39) |
V205E |
probably benign |
Het |
| Tmcc1 |
C |
CAT |
6: 116,019,831 (GRCm39) |
|
probably null |
Het |
| Tnfaip6 |
G |
A |
2: 51,940,926 (GRCm39) |
D156N |
probably benign |
Het |
| Uggt2 |
T |
A |
14: 119,232,461 (GRCm39) |
E1463D |
probably damaging |
Het |
| Urb2 |
C |
A |
8: 124,756,878 (GRCm39) |
P862T |
probably benign |
Het |
| Vmn1r64 |
A |
T |
7: 5,887,369 (GRCm39) |
L58* |
probably null |
Het |
| Vmn2r3 |
C |
A |
3: 64,166,483 (GRCm39) |
G883C |
probably benign |
Het |
| Vps13d |
A |
T |
4: 144,837,465 (GRCm39) |
C2707S |
possibly damaging |
Het |
| Wdr11 |
G |
T |
7: 129,207,418 (GRCm39) |
|
probably null |
Het |
| Wdr37 |
T |
A |
13: 8,911,268 (GRCm39) |
|
probably benign |
Het |
| Wtap |
G |
A |
17: 13,194,352 (GRCm39) |
Q95* |
probably null |
Het |
| Zfp26 |
A |
T |
9: 20,348,563 (GRCm39) |
L667H |
probably damaging |
Het |
| Zfp268 |
C |
T |
4: 145,311,891 (GRCm39) |
|
probably benign |
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 |
|
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'- TCCCAAGATCAGGATTGGCC -3'
(R):5'- TGACCTACCACTGAGCTGTC -3'
Sequencing Primer
(F):5'- TCAGGATTGGCCAAGATGACTTACC -3'
(R):5'- TTGTAAGGCTGTGGATCC -3'
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| Posted On |
2014-10-15 |
Incidental Mutation