Incidental Mutation 'R7177:Col9a1'
ID |
558655 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col9a1
|
Ensembl Gene |
ENSMUSG00000026147 |
Gene Name |
collagen, type IX, alpha 1 |
Synonyms |
Col9a-1 |
MMRRC Submission |
045268-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.092)
|
Stock # |
R7177 (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 24234498 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Leucine to Glutamine
at position 13
(L13Q)
|
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 |
unknown
Transcript: ENSMUST00000088349
AA Change: L13Q
|
SMART Domains |
Protein: ENSMUSP00000085687 Gene: ENSMUSG00000026147 AA Change: L13Q
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 |
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 98.9%
|
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: 75 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930550C14Rik |
T |
C |
9: 53,325,685 (GRCm39) |
L74S |
probably damaging |
Het |
5730409E04Rik |
A |
G |
4: 126,505,525 (GRCm39) |
S18G |
probably benign |
Het |
Adam29 |
A |
G |
8: 56,325,659 (GRCm39) |
I265T |
probably benign |
Het |
Aff4 |
C |
T |
11: 53,297,466 (GRCm39) |
S896L |
probably benign |
Het |
Ankrd27 |
T |
C |
7: 35,318,822 (GRCm39) |
I571T |
probably damaging |
Het |
Bdp1 |
C |
A |
13: 100,186,478 (GRCm39) |
R1658I |
probably damaging |
Het |
Carm1 |
C |
T |
9: 21,458,323 (GRCm39) |
T7M |
unknown |
Het |
Ccdc183 |
A |
G |
2: 25,506,296 (GRCm39) |
V100A |
probably damaging |
Het |
Cd86 |
CA |
CAA |
16: 36,426,917 (GRCm39) |
|
probably null |
Het |
Ceacam2 |
T |
G |
7: 25,220,341 (GRCm39) |
D239A |
probably benign |
Het |
Cfap96 |
T |
A |
8: 46,423,444 (GRCm39) |
E89D |
possibly damaging |
Het |
Cimap1c |
T |
A |
9: 56,757,262 (GRCm39) |
M139L |
possibly damaging |
Het |
Cmya5 |
T |
C |
13: 93,231,836 (GRCm39) |
D1084G |
probably benign |
Het |
Cog5 |
T |
A |
12: 31,810,888 (GRCm39) |
I194K |
probably damaging |
Het |
Col20a1 |
C |
T |
2: 180,636,007 (GRCm39) |
Q211* |
probably null |
Het |
Cracr2a |
A |
T |
6: 127,585,669 (GRCm39) |
M156L |
probably benign |
Het |
Cts8 |
C |
T |
13: 61,399,505 (GRCm39) |
M151I |
possibly damaging |
Het |
Cyp2ab1 |
A |
T |
16: 20,135,469 (GRCm39) |
L11Q |
probably null |
Het |
Dhrs13 |
T |
A |
11: 77,925,208 (GRCm39) |
C160S |
probably benign |
Het |
Enthd1 |
T |
A |
15: 80,358,415 (GRCm39) |
E368D |
probably damaging |
Het |
Fbh1 |
A |
G |
2: 11,760,522 (GRCm39) |
I676T |
probably damaging |
Het |
Fcgrt |
T |
C |
7: 44,751,421 (GRCm39) |
R176G |
probably benign |
Het |
Gatd1 |
A |
G |
7: 140,990,947 (GRCm39) |
F67L |
possibly damaging |
Het |
Gm4353 |
G |
A |
7: 115,683,727 (GRCm39) |
P23S |
probably damaging |
Het |
Gm6882 |
T |
A |
7: 21,161,677 (GRCm39) |
I64F |
possibly damaging |
Het |
Grwd1 |
A |
T |
7: 45,480,204 (GRCm39) |
M1K |
probably null |
Het |
Hook2 |
T |
A |
8: 85,718,046 (GRCm39) |
S58T |
probably benign |
Het |
Iqch |
T |
G |
9: 63,329,117 (GRCm39) |
*1072C |
probably null |
Het |
Kmt2d |
G |
A |
15: 98,748,267 (GRCm39) |
T3019I |
unknown |
Het |
Lmx1a |
T |
C |
1: 167,674,247 (GRCm39) |
S356P |
probably benign |
Het |
Lrig3 |
A |
G |
10: 125,842,712 (GRCm39) |
M546V |
probably benign |
Het |
Lrrc1 |
C |
A |
9: 77,379,504 (GRCm39) |
E96* |
probably null |
Het |
Lrtm2 |
C |
A |
6: 119,294,113 (GRCm39) |
M339I |
probably damaging |
Het |
Map10 |
T |
C |
8: 126,398,584 (GRCm39) |
V659A |
probably benign |
Het |
Map7d1 |
A |
G |
4: 126,130,778 (GRCm39) |
C384R |
probably damaging |
Het |
Mcur1 |
T |
C |
13: 43,698,012 (GRCm39) |
D296G |
probably damaging |
Het |
Mettl24 |
A |
T |
10: 40,686,508 (GRCm39) |
H295L |
probably damaging |
Het |
Mgat4f |
T |
C |
1: 134,318,163 (GRCm39) |
S312P |
probably benign |
Het |
Mpl |
A |
G |
4: 118,305,741 (GRCm39) |
|
probably null |
Het |
Mrps5 |
T |
C |
2: 127,437,617 (GRCm39) |
V148A |
probably benign |
Het |
N4bp2 |
T |
C |
5: 65,964,891 (GRCm39) |
V980A |
probably damaging |
Het |
Ncaph |
A |
T |
2: 126,958,506 (GRCm39) |
D504E |
probably damaging |
Het |
Nxph1 |
A |
G |
6: 9,247,497 (GRCm39) |
N156S |
probably damaging |
Het |
Or2t26 |
T |
A |
11: 49,040,012 (GRCm39) |
C309* |
probably null |
Het |
Or4f14b |
T |
A |
2: 111,775,501 (GRCm39) |
Q100L |
probably damaging |
Het |
Pafah1b3 |
T |
A |
7: 24,994,657 (GRCm39) |
I186L |
probably benign |
Het |
Papola |
C |
A |
12: 105,775,790 (GRCm39) |
N235K |
possibly damaging |
Het |
Pcnx3 |
A |
T |
19: 5,737,527 (GRCm39) |
M98K |
probably benign |
Het |
Pip4p1 |
A |
C |
14: 51,167,634 (GRCm39) |
M104R |
possibly damaging |
Het |
Pkhd1l1 |
A |
G |
15: 44,330,800 (GRCm39) |
N125S |
probably damaging |
Het |
Pls1 |
T |
A |
9: 95,655,612 (GRCm39) |
H380L |
probably benign |
Het |
Plxna1 |
T |
C |
6: 89,300,311 (GRCm39) |
T1591A |
possibly damaging |
Het |
Pparg |
T |
G |
6: 115,418,581 (GRCm39) |
S147A |
probably benign |
Het |
Prdm10 |
T |
C |
9: 31,279,003 (GRCm39) |
S1025P |
probably benign |
Het |
Prkcd |
T |
A |
14: 30,321,664 (GRCm39) |
H510L |
probably damaging |
Het |
Ptprh |
T |
A |
7: 4,572,480 (GRCm39) |
E499D |
possibly damaging |
Het |
Rad51ap1 |
A |
G |
6: 126,901,983 (GRCm39) |
S256P |
probably benign |
Het |
Rad54b |
A |
G |
4: 11,599,755 (GRCm39) |
T320A |
probably damaging |
Het |
Rnf207 |
A |
G |
4: 152,396,634 (GRCm39) |
I459T |
probably benign |
Het |
Runx2 |
G |
A |
17: 45,125,079 (GRCm39) |
P80L |
probably damaging |
Het |
Ryr3 |
A |
T |
2: 112,731,188 (GRCm39) |
D727E |
probably damaging |
Het |
Sdk2 |
C |
T |
11: 113,720,795 (GRCm39) |
R1378H |
possibly damaging |
Het |
Slc7a11 |
A |
G |
3: 50,397,680 (GRCm39) |
S11P |
probably benign |
Het |
Sox4 |
A |
G |
13: 29,137,000 (GRCm39) |
V2A |
probably damaging |
Het |
Srf |
A |
G |
17: 46,866,318 (GRCm39) |
F146S |
probably damaging |
Het |
Srrm2 |
T |
C |
17: 24,035,747 (GRCm39) |
V797A |
unknown |
Het |
Stk32c |
T |
C |
7: 138,684,218 (GRCm39) |
D463G |
possibly damaging |
Het |
Syne2 |
C |
A |
12: 76,018,654 (GRCm39) |
Y3384* |
probably null |
Het |
Tektl1 |
T |
C |
10: 78,588,324 (GRCm39) |
D162G |
probably damaging |
Het |
Traip |
T |
A |
9: 107,838,184 (GRCm39) |
M139K |
possibly damaging |
Het |
Trappc2l |
T |
A |
8: 123,341,051 (GRCm39) |
F100Y |
probably damaging |
Het |
Ush1c |
T |
C |
7: 45,878,643 (GRCm39) |
D124G |
probably damaging |
Het |
Uty |
A |
G |
Y: 1,099,691 (GRCm39) |
V1168A |
probably benign |
Het |
Vmn2r25 |
T |
C |
6: 123,816,882 (GRCm39) |
D233G |
possibly damaging |
Het |
Zdbf2 |
C |
T |
1: 63,334,120 (GRCm39) |
R31C |
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 |
|
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 |
|
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'- AAGAAACCCAGGTCCCCTTG -3'
(R):5'- GGGTACTCTGACTTCTCACACC -3'
Sequencing Primer
(F):5'- TTGGCCAGGCACCTTTG -3'
(R):5'- GTACTCTGACTTCTCACACCCAGAAC -3'
|
Posted On |
2019-06-26 |