Incidental Mutation 'R5519:Col9a1'
ID |
431442 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col9a1
|
Ensembl Gene |
ENSMUSG00000026147 |
Gene Name |
collagen, type IX, alpha 1 |
Synonyms |
Col9a-1 |
MMRRC Submission |
043078-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.092)
|
Stock # |
R5519 (G1)
|
Quality Score |
194 |
Status
|
Not validated
|
Chromosome |
1 |
Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
Type of Mutation |
splice site (5 bp from exon) |
DNA Base Change (assembly) |
G to A
at 24269335 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Ref Sequence |
ENSEMBL: ENSMUSP00000085687
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000054588]
[ENSMUST00000088349]
|
AlphaFold |
no structure available at present |
Predicted Effect |
probably null
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 |
probably null
Transcript: ENSMUST00000088349
|
SMART Domains |
Protein: ENSMUSP00000085687 Gene: ENSMUSG00000026147
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 |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147902
|
Coding Region Coverage |
- 1x: 99.1%
- 3x: 97.6%
- 10x: 94.7%
- 20x: 88.5%
|
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: 36 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700067K01Rik |
T |
C |
8: 84,729,621 (GRCm39) |
V99A |
possibly damaging |
Het |
2510009E07Rik |
A |
G |
16: 21,472,218 (GRCm39) |
S91P |
probably benign |
Het |
2810021J22Rik |
G |
A |
11: 58,770,923 (GRCm39) |
S135N |
probably benign |
Het |
A530084C06Rik |
T |
C |
13: 31,742,702 (GRCm39) |
|
probably benign |
Het |
Acadsb |
T |
C |
7: 131,031,694 (GRCm39) |
S177P |
probably damaging |
Het |
Acp3 |
C |
A |
9: 104,168,687 (GRCm39) |
G393W |
probably damaging |
Het |
Axl |
G |
A |
7: 25,478,087 (GRCm39) |
A204V |
possibly damaging |
Het |
Birc6 |
A |
T |
17: 74,887,173 (GRCm39) |
M806L |
probably benign |
Het |
Cacna1i |
T |
C |
15: 80,255,700 (GRCm39) |
L861P |
probably damaging |
Het |
Cfap44 |
A |
T |
16: 44,224,451 (GRCm39) |
D53V |
probably damaging |
Het |
Ctf2 |
T |
A |
7: 127,318,463 (GRCm39) |
I179L |
probably benign |
Het |
Cybb |
C |
G |
X: 9,316,989 (GRCm39) |
D246H |
probably benign |
Het |
Emilin2 |
G |
A |
17: 71,559,930 (GRCm39) |
P1016S |
probably benign |
Het |
Gm12790 |
G |
A |
4: 101,824,888 (GRCm39) |
P127S |
probably benign |
Het |
Gsap |
T |
A |
5: 21,494,857 (GRCm39) |
V24E |
probably damaging |
Het |
Ipp |
T |
C |
4: 116,367,964 (GRCm39) |
F66L |
possibly damaging |
Het |
Jakmip3 |
T |
C |
7: 138,609,520 (GRCm39) |
I208T |
probably damaging |
Het |
Med30 |
G |
T |
15: 52,584,462 (GRCm39) |
D127Y |
probably damaging |
Het |
Mosmo |
C |
T |
7: 120,329,733 (GRCm39) |
P118L |
probably benign |
Het |
Ncam2 |
C |
T |
16: 81,231,766 (GRCm39) |
R77* |
probably null |
Het |
Nfkb2 |
G |
T |
19: 46,296,006 (GRCm39) |
E170D |
probably benign |
Het |
Or51a42 |
G |
A |
7: 103,708,504 (GRCm39) |
Q102* |
probably null |
Het |
Padi2 |
A |
G |
4: 140,676,533 (GRCm39) |
D557G |
probably damaging |
Het |
Pde11a |
T |
A |
2: 75,906,299 (GRCm39) |
K639N |
probably damaging |
Het |
Pspc1 |
T |
C |
14: 57,009,413 (GRCm39) |
I140M |
probably benign |
Het |
Rundc3a |
A |
T |
11: 102,292,857 (GRCm39) |
I417F |
probably benign |
Het |
Scn1a |
T |
A |
2: 66,162,557 (GRCm39) |
I230F |
probably damaging |
Het |
Serpinb3b |
A |
G |
1: 107,087,506 (GRCm39) |
M1T |
probably null |
Het |
Sin3a |
T |
C |
9: 57,025,457 (GRCm39) |
|
probably null |
Het |
St8sia1 |
T |
C |
6: 142,909,287 (GRCm39) |
N70D |
probably damaging |
Het |
Tdpoz4 |
A |
T |
3: 93,704,806 (GRCm39) |
T368S |
probably benign |
Het |
Tpm2 |
T |
G |
4: 43,522,751 (GRCm39) |
D55A |
possibly damaging |
Het |
Trdv1 |
T |
A |
14: 54,119,405 (GRCm39) |
M22K |
probably benign |
Het |
Zc3h4 |
A |
T |
7: 16,169,157 (GRCm39) |
T1089S |
unknown |
Het |
Zfp518b |
G |
A |
5: 38,831,441 (GRCm39) |
T188M |
probably damaging |
Het |
Zfp74 |
G |
T |
7: 29,634,559 (GRCm39) |
A383D |
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 |
|
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'- AGTGATGGGAGATTTTGGCAAC -3'
(R):5'- TGCATTCTACAAGCCACGCTG -3'
Sequencing Primer
(F):5'- CACCTATATTTTACCAAAAGCCTGG -3'
(R):5'- GCCACGCTGATTAAAATACTCATG -3'
|
Posted On |
2016-10-05 |