Incidental Mutation 'R3757:Col9a1'
ID |
271464 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col9a1
|
Ensembl Gene |
ENSMUSG00000026147 |
Gene Name |
collagen, type IX, alpha 1 |
Synonyms |
Col9a-1 |
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.121)
|
Stock # |
R3757 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
1 |
Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
Type of Mutation |
critical splice donor site (2 bp from exon) |
DNA Base Change (assembly) |
T to C
at 24271312 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
|
Meta Mutation Damage Score |
0.9474 |
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.3%
|
Validation Efficiency |
92% (35/38) |
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 |
Adamtsl3 |
T |
A |
7: 81,986,415 (GRCm39) |
I9K |
probably benign |
Het |
Arhgap31 |
T |
C |
16: 38,457,362 (GRCm39) |
E82G |
probably damaging |
Het |
Asap2 |
T |
A |
12: 21,317,767 (GRCm39) |
S993T |
probably damaging |
Het |
Bmpr1a |
A |
T |
14: 34,156,624 (GRCm39) |
L134* |
probably null |
Het |
Cacna1e |
A |
G |
1: 154,509,442 (GRCm39) |
V271A |
probably damaging |
Het |
Cacna2d4 |
A |
G |
6: 119,218,124 (GRCm39) |
E153G |
probably damaging |
Het |
Cage1 |
A |
C |
13: 38,209,705 (GRCm39) |
F91V |
possibly damaging |
Het |
Cdh24 |
T |
C |
14: 54,869,637 (GRCm39) |
D760G |
possibly damaging |
Het |
Cts6 |
A |
T |
13: 61,349,972 (GRCm39) |
Y36* |
probably null |
Het |
Dennd3 |
C |
G |
15: 73,394,083 (GRCm39) |
A36G |
probably benign |
Het |
Dmxl1 |
G |
A |
18: 50,068,384 (GRCm39) |
G2719D |
probably damaging |
Het |
Dnajc28 |
G |
A |
16: 91,413,755 (GRCm39) |
T187M |
probably damaging |
Het |
Ep300 |
T |
A |
15: 81,532,790 (GRCm39) |
V1676E |
unknown |
Het |
Ercc4 |
C |
T |
16: 12,962,360 (GRCm39) |
T668M |
probably benign |
Het |
G530012D18Rik |
CAGAGAGA |
CAGAGAGAGA |
1: 85,504,945 (GRCm39) |
|
probably null |
Het |
Gm10985 |
GCTCTCTCTCTCTCTCTCTCTCTCTCTCT |
GCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT |
3: 53,752,645 (GRCm39) |
|
probably null |
Het |
H1f4 |
T |
A |
13: 23,806,240 (GRCm39) |
K81* |
probably null |
Het |
Havcr1 |
G |
T |
11: 46,643,407 (GRCm39) |
R109L |
probably damaging |
Het |
Krtap4-9 |
A |
G |
11: 99,676,444 (GRCm39) |
|
probably benign |
Het |
Layn |
T |
C |
9: 50,970,856 (GRCm39) |
E229G |
probably benign |
Het |
Lpcat3 |
T |
A |
6: 124,676,955 (GRCm39) |
|
probably null |
Het |
Lrrn1 |
T |
A |
6: 107,546,169 (GRCm39) |
F656I |
possibly damaging |
Het |
Lypd1 |
A |
G |
1: 125,838,121 (GRCm39) |
|
probably benign |
Het |
Or4k41 |
T |
A |
2: 111,279,602 (GRCm39) |
V39E |
possibly damaging |
Het |
Or5v1b |
T |
A |
17: 37,841,246 (GRCm39) |
I126N |
probably damaging |
Het |
Or6c207 |
T |
C |
10: 129,104,934 (GRCm39) |
D86G |
probably damaging |
Het |
Ptprt |
A |
T |
2: 161,653,950 (GRCm39) |
L560Q |
probably damaging |
Het |
Rbm11 |
T |
C |
16: 75,393,469 (GRCm39) |
V55A |
probably damaging |
Het |
Scn11a |
C |
T |
9: 119,632,569 (GRCm39) |
V434I |
probably benign |
Het |
Serpinc1 |
A |
G |
1: 160,829,935 (GRCm39) |
T434A |
probably benign |
Het |
Setd2 |
T |
C |
9: 110,402,753 (GRCm39) |
I1798T |
probably damaging |
Het |
Sfswap |
A |
G |
5: 129,590,298 (GRCm39) |
Y265C |
probably damaging |
Het |
Slc9a8 |
C |
A |
2: 167,266,050 (GRCm39) |
T9K |
probably benign |
Het |
Synpo |
T |
C |
18: 60,736,062 (GRCm39) |
D389G |
probably damaging |
Het |
Vmn1r181 |
C |
T |
7: 23,683,909 (GRCm39) |
L125F |
possibly damaging |
Het |
Wdfy4 |
A |
C |
14: 32,745,331 (GRCm39) |
H2296Q |
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 |
R2240:Col9a1
|
UTSW |
1 |
24,218,582 (GRCm39) |
missense |
unknown |
|
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'- GAGCTCCTGAATGACCCTTG -3'
(R):5'- GCTTAAATGTCTCACTGTAAGACCAC -3'
Sequencing Primer
(F):5'- CCCTTGGGGCATTTGGC -3'
(R):5'- ATCTAAAGCTAGGTCTACCTATCTGC -3'
|
Posted On |
2015-03-18 |