Incidental Mutation 'R5511:Col9a1'
| ID |
431196 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
043072-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.092)
|
| Stock # |
R5511 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 24218619 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 77
(V77A)
|
| 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: V77A
|
| SMART Domains |
Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: V77A
| 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 |
|
| Meta Mutation Damage Score |
0.1036 |
| Coding Region Coverage |
- 1x: 98.5%
- 3x: 97.4%
- 10x: 95.1%
- 20x: 90.3%
|
| Validation Efficiency |
98% (81/83) |
| 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: 70 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aadacl2fm2 |
T |
C |
3: 59,654,685 (GRCm39) |
L173P |
probably damaging |
Het |
| Agl |
A |
T |
3: 116,582,209 (GRCm39) |
V271D |
possibly damaging |
Het |
| Alox15 |
G |
T |
11: 70,240,808 (GRCm39) |
P191T |
probably benign |
Het |
| Apaf1 |
T |
C |
10: 90,890,254 (GRCm39) |
Y583C |
probably damaging |
Het |
| Aqp9 |
T |
A |
9: 71,070,375 (GRCm39) |
|
probably benign |
Het |
| Bms1 |
A |
G |
6: 118,365,848 (GRCm39) |
F1113L |
possibly damaging |
Het |
| Cap1 |
A |
C |
4: 122,756,583 (GRCm39) |
|
probably benign |
Het |
| Car11 |
T |
C |
7: 45,349,885 (GRCm39) |
W35R |
probably damaging |
Het |
| Casc3 |
T |
A |
11: 98,701,740 (GRCm39) |
Y91* |
probably null |
Het |
| Ccdc192 |
G |
A |
18: 57,671,156 (GRCm39) |
|
probably null |
Het |
| Cd22 |
A |
T |
7: 30,569,496 (GRCm39) |
I540N |
probably damaging |
Het |
| Chad |
A |
T |
11: 94,456,072 (GRCm39) |
E50V |
probably damaging |
Het |
| Chd3 |
C |
G |
11: 69,252,301 (GRCm39) |
G34R |
probably damaging |
Het |
| Copg1 |
G |
A |
6: 87,889,276 (GRCm39) |
V873M |
probably damaging |
Het |
| Dnhd1 |
T |
A |
7: 105,363,363 (GRCm39) |
V3975E |
probably damaging |
Het |
| Dock6 |
A |
T |
9: 21,728,703 (GRCm39) |
V1290D |
possibly damaging |
Het |
| Elp2 |
A |
T |
18: 24,745,507 (GRCm39) |
K150* |
probably null |
Het |
| Eri3 |
A |
C |
4: 117,472,386 (GRCm39) |
Y260S |
possibly damaging |
Het |
| Esrrg |
C |
T |
1: 187,943,304 (GRCm39) |
L426F |
probably damaging |
Het |
| Farp1 |
G |
T |
14: 121,474,584 (GRCm39) |
V266L |
probably damaging |
Het |
| Flnc |
A |
G |
6: 29,458,897 (GRCm39) |
E2459G |
probably damaging |
Het |
| Glis1 |
G |
A |
4: 107,293,074 (GRCm39) |
D66N |
probably damaging |
Het |
| Gm14129 |
T |
A |
2: 148,773,446 (GRCm39) |
|
noncoding transcript |
Het |
| Gm28051 |
A |
G |
12: 102,686,415 (GRCm39) |
*82R |
probably null |
Het |
| Gm8741 |
G |
T |
17: 35,555,062 (GRCm39) |
|
noncoding transcript |
Het |
| Gne |
C |
T |
4: 44,041,843 (GRCm39) |
V485M |
probably damaging |
Het |
| Lcn10 |
T |
A |
2: 25,572,841 (GRCm39) |
V15E |
probably benign |
Het |
| Mapk11 |
T |
A |
15: 89,029,380 (GRCm39) |
|
probably null |
Het |
| Me3 |
T |
G |
7: 89,455,876 (GRCm39) |
Y243D |
probably damaging |
Het |
| Mllt6 |
G |
A |
11: 97,560,326 (GRCm39) |
S210N |
possibly damaging |
Het |
| Myo1h |
T |
A |
5: 114,483,958 (GRCm39) |
L519* |
probably null |
Het |
| Myo9a |
T |
C |
9: 59,687,495 (GRCm39) |
V200A |
probably damaging |
Het |
| Mzf1 |
T |
A |
7: 12,785,526 (GRCm39) |
Q161H |
possibly damaging |
Het |
| Nim1k |
T |
G |
13: 120,189,130 (GRCm39) |
H93P |
probably damaging |
Het |
| Nkx6-1 |
C |
A |
5: 101,811,532 (GRCm39) |
R190L |
probably damaging |
Het |
| Noc3l |
A |
G |
19: 38,782,625 (GRCm39) |
V671A |
probably benign |
Het |
| Nsd1 |
T |
C |
13: 55,460,543 (GRCm39) |
S2257P |
probably benign |
Het |
| Nup210 |
T |
A |
6: 91,003,945 (GRCm39) |
I648F |
probably damaging |
Het |
| Oplah |
T |
C |
15: 76,189,944 (GRCm39) |
E223G |
possibly damaging |
Het |
| Or5b120 |
T |
C |
19: 13,480,556 (GRCm39) |
M283T |
probably benign |
Het |
| Plekhs1 |
A |
C |
19: 56,474,224 (GRCm39) |
T457P |
probably damaging |
Het |
| Plppr4 |
G |
A |
3: 117,119,551 (GRCm39) |
T286I |
probably benign |
Het |
| Prpf4b |
T |
C |
13: 35,068,037 (GRCm39) |
|
probably benign |
Het |
| Prss39 |
T |
A |
1: 34,541,878 (GRCm39) |
D318E |
possibly damaging |
Het |
| Psap |
A |
G |
10: 60,134,959 (GRCm39) |
E289G |
possibly damaging |
Het |
| Rad17 |
A |
G |
13: 100,764,157 (GRCm39) |
V438A |
possibly damaging |
Het |
| Raf1 |
T |
C |
6: 115,597,217 (GRCm39) |
S28G |
probably benign |
Het |
| Ranbp2 |
A |
G |
10: 58,329,561 (GRCm39) |
D2978G |
probably benign |
Het |
| Rnf170 |
T |
A |
8: 26,631,027 (GRCm39) |
D213E |
probably damaging |
Het |
| Rsph3a |
T |
A |
17: 8,164,905 (GRCm39) |
H88Q |
possibly damaging |
Het |
| Scd1 |
A |
G |
19: 44,395,198 (GRCm39) |
I9T |
probably benign |
Het |
| Sgk3 |
T |
C |
1: 9,968,911 (GRCm39) |
|
probably benign |
Het |
| Slc14a1 |
C |
T |
18: 78,145,686 (GRCm39) |
S416N |
probably benign |
Het |
| Smok4a |
T |
C |
17: 13,746,474 (GRCm39) |
|
noncoding transcript |
Het |
| Sostdc1 |
A |
T |
12: 36,367,165 (GRCm39) |
I114F |
probably damaging |
Het |
| Spen |
G |
A |
4: 141,202,375 (GRCm39) |
T2084I |
possibly damaging |
Het |
| Spen |
G |
T |
4: 141,244,149 (GRCm39) |
D295E |
unknown |
Het |
| Sptbn5 |
T |
C |
2: 119,890,202 (GRCm39) |
|
probably benign |
Het |
| Srebf1 |
T |
C |
11: 60,101,184 (GRCm39) |
|
probably benign |
Het |
| Tcea3 |
A |
T |
4: 135,998,683 (GRCm39) |
Y319F |
probably damaging |
Het |
| Timd4 |
T |
A |
11: 46,710,807 (GRCm39) |
|
probably null |
Het |
| Tmem88b |
G |
A |
4: 155,870,002 (GRCm39) |
P20S |
probably damaging |
Het |
| Tsen2 |
T |
A |
6: 115,538,365 (GRCm39) |
C281S |
probably damaging |
Het |
| Vmn2r28 |
T |
C |
7: 5,487,011 (GRCm39) |
T551A |
possibly damaging |
Het |
| Vmn2r45 |
T |
C |
7: 8,474,832 (GRCm39) |
H732R |
probably benign |
Het |
| Wdr90 |
A |
G |
17: 26,063,995 (GRCm39) |
|
probably benign |
Het |
| Zdbf2 |
T |
C |
1: 63,344,836 (GRCm39) |
S1072P |
probably benign |
Het |
| Zfp148 |
A |
G |
16: 33,255,004 (GRCm39) |
|
probably benign |
Het |
| Zfp2 |
T |
A |
11: 50,790,851 (GRCm39) |
E397D |
probably damaging |
Het |
| Zfp729b |
A |
G |
13: 67,740,499 (GRCm39) |
F599L |
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 |
|
|
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'- TGACTTACCAGGCAAGTAGC -3'
(R):5'- TACCACTGAGCTGTCCTCCAAG -3'
Sequencing Primer
(F):5'- AGTAGCACTGCATCATACTGG -3'
(R):5'- CCTTGTTGGAATCCTGAAG -3'
|
| Posted On |
2016-10-05 |
Incidental Mutation