Incidental Mutation 'R5144:Col9a1'
ID |
395026 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col9a1
|
Ensembl Gene |
ENSMUSG00000026147 |
Gene Name |
collagen, type IX, alpha 1 |
Synonyms |
Col9a-1 |
MMRRC Submission |
042728-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.092)
|
Stock # |
R5144 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
1 |
Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 24278434 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Isoleucine to Valine
at position 821
(I821V)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000051579
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000054588]
[ENSMUST00000088349]
|
AlphaFold |
no structure available at present |
Predicted Effect |
probably benign
Transcript: ENSMUST00000054588
AA Change: I821V
PolyPhen 2
Score 0.079 (Sensitivity: 0.93; Specificity: 0.85)
|
SMART Domains |
Protein: ENSMUSP00000051579 Gene: ENSMUSG00000026147 AA Change: I821V
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 |
probably benign
Transcript: ENSMUST00000088349
AA Change: I580V
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
SMART Domains |
Protein: ENSMUSP00000085687 Gene: ENSMUSG00000026147 AA Change: I580V
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 |
|
Meta Mutation Damage Score |
0.0623 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.9%
- 20x: 94.1%
|
Validation Efficiency |
96% (47/49) |
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: 44 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4933409G03Rik |
T |
A |
2: 68,446,604 (GRCm39) |
|
probably benign |
Het |
Arpc2 |
A |
T |
1: 74,287,367 (GRCm39) |
K62N |
probably damaging |
Het |
B4galt5 |
C |
T |
2: 167,148,516 (GRCm39) |
E201K |
possibly damaging |
Het |
Bub1b |
C |
T |
2: 118,445,980 (GRCm39) |
T334M |
possibly damaging |
Het |
Ccdc71 |
T |
C |
9: 108,341,051 (GRCm39) |
V288A |
probably benign |
Het |
Cep350 |
G |
A |
1: 155,786,896 (GRCm39) |
R1444W |
probably damaging |
Het |
Chrna4 |
A |
G |
2: 180,666,623 (GRCm39) |
L605P |
probably damaging |
Het |
Col6a5 |
T |
A |
9: 105,766,482 (GRCm39) |
I1813F |
probably damaging |
Het |
D430041D05Rik |
T |
C |
2: 104,088,847 (GRCm39) |
D43G |
probably damaging |
Het |
Depdc7 |
T |
C |
2: 104,560,598 (GRCm39) |
Y132C |
probably damaging |
Het |
Dppa2 |
T |
C |
16: 48,137,666 (GRCm39) |
V216A |
probably damaging |
Het |
Ect2l |
A |
T |
10: 18,020,325 (GRCm39) |
N598K |
probably benign |
Het |
Eif3c |
T |
C |
7: 126,162,238 (GRCm39) |
T195A |
probably benign |
Het |
Epg5 |
T |
C |
18: 78,058,895 (GRCm39) |
V1883A |
probably damaging |
Het |
Ino80c |
T |
A |
18: 24,241,935 (GRCm39) |
D150V |
probably benign |
Het |
Kcnb1 |
T |
A |
2: 166,947,864 (GRCm39) |
Y328F |
probably damaging |
Het |
Kcnj3 |
G |
A |
2: 55,337,059 (GRCm39) |
|
probably null |
Het |
Ncor1 |
T |
G |
11: 62,240,290 (GRCm39) |
S894R |
probably damaging |
Het |
Nlgn3 |
G |
A |
X: 100,361,891 (GRCm39) |
V287I |
probably benign |
Het |
Nod2 |
T |
C |
8: 89,379,694 (GRCm39) |
V72A |
probably damaging |
Het |
Nudt19 |
T |
C |
7: 35,254,650 (GRCm39) |
T194A |
probably benign |
Het |
Or1j4 |
A |
T |
2: 36,740,156 (GRCm39) |
T33S |
probably benign |
Het |
Or8b53 |
C |
T |
9: 38,667,689 (GRCm39) |
S235L |
possibly damaging |
Het |
Pappa2 |
T |
A |
1: 158,784,703 (GRCm39) |
R102S |
probably benign |
Het |
Pik3c2a |
T |
C |
7: 115,950,021 (GRCm39) |
N1332S |
probably benign |
Het |
Plppr1 |
T |
A |
4: 49,319,800 (GRCm39) |
V142E |
possibly damaging |
Het |
Prdm6 |
C |
A |
18: 53,598,110 (GRCm39) |
|
probably benign |
Het |
Prm2 |
T |
A |
16: 10,609,732 (GRCm39) |
|
probably benign |
Het |
Prmt3 |
T |
C |
7: 49,435,883 (GRCm39) |
S155P |
possibly damaging |
Het |
Rars2 |
T |
C |
4: 34,656,793 (GRCm39) |
Y481H |
probably benign |
Het |
Rgs2 |
G |
A |
1: 143,877,437 (GRCm39) |
T206M |
probably benign |
Het |
Slc2a8 |
C |
T |
2: 32,871,785 (GRCm39) |
R56H |
probably damaging |
Het |
Spmip11 |
C |
A |
15: 98,483,148 (GRCm39) |
|
probably null |
Het |
Stk35 |
T |
A |
2: 129,652,855 (GRCm39) |
M452K |
probably damaging |
Het |
Tcf3 |
G |
A |
10: 80,251,071 (GRCm39) |
H454Y |
probably damaging |
Het |
Tgm3 |
C |
T |
2: 129,890,202 (GRCm39) |
S655F |
possibly damaging |
Het |
Tssc4 |
T |
G |
7: 142,623,770 (GRCm39) |
L26R |
probably damaging |
Het |
Utp11 |
A |
T |
4: 124,572,695 (GRCm39) |
|
probably benign |
Het |
Vmn1r237 |
C |
G |
17: 21,534,688 (GRCm39) |
A137G |
possibly damaging |
Het |
Vmn2r129 |
G |
T |
4: 156,686,692 (GRCm39) |
|
noncoding transcript |
Het |
Vps8 |
T |
C |
16: 21,378,103 (GRCm39) |
L1038P |
probably damaging |
Het |
Wipf3 |
C |
T |
6: 54,462,660 (GRCm39) |
A290V |
probably damaging |
Het |
Zdhhc25 |
T |
G |
15: 88,485,259 (GRCm39) |
L198R |
probably damaging |
Het |
Zdhhc6 |
A |
T |
19: 55,302,998 (GRCm39) |
M1K |
probably null |
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 |
|
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'- AAGCCAATGTTGTGATGGTGAC -3'
(R):5'- CTTGTACCTGGCAAAATAGCTTAC -3'
Sequencing Primer
(F):5'- AGCCAATGTTGTGATGGTGACTTATG -3'
(R):5'- ATACGCTGTTGTGAAAGGCC -3'
|
Posted On |
2016-06-21 |