Incidental Mutation 'R6478:Col9a1'
| ID |
516876 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
044610-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.092)
|
| Stock # |
R6478 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 24224486 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Isoleucine
at position 223
(L223I)
|
| 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: L223I
|
| SMART Domains |
Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: L223I
| 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 |
0.0653 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 97.8%
- 20x: 93.3%
|
| Validation Efficiency |
95% (75/79) |
| 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: 78 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aatk |
T |
A |
11: 119,901,817 (GRCm39) |
S803C |
probably benign |
Het |
| Abcc9 |
C |
T |
6: 142,625,034 (GRCm39) |
A454T |
probably damaging |
Het |
| Abr |
T |
C |
11: 76,343,158 (GRCm39) |
E565G |
probably damaging |
Het |
| Adam33 |
C |
A |
2: 130,893,266 (GRCm39) |
R753L |
probably benign |
Het |
| Adgre1 |
A |
G |
17: 57,708,955 (GRCm39) |
T49A |
possibly damaging |
Het |
| Ankra2 |
A |
T |
13: 98,404,950 (GRCm39) |
H153L |
probably damaging |
Het |
| Ankrd26 |
T |
G |
6: 118,488,599 (GRCm39) |
E1353D |
probably benign |
Het |
| Ankrd52 |
T |
G |
10: 128,215,200 (GRCm39) |
|
probably null |
Het |
| Arhgef10l |
T |
A |
4: 140,270,068 (GRCm39) |
T619S |
possibly damaging |
Het |
| Armh4 |
A |
G |
14: 50,010,789 (GRCm39) |
V306A |
possibly damaging |
Het |
| Asgr1 |
T |
C |
11: 69,947,720 (GRCm39) |
V130A |
possibly damaging |
Het |
| Atg10 |
C |
A |
13: 91,085,466 (GRCm39) |
C161F |
probably damaging |
Het |
| Atm |
A |
T |
9: 53,401,554 (GRCm39) |
N1438K |
probably damaging |
Het |
| BC107364 |
T |
A |
3: 96,343,322 (GRCm39) |
|
probably null |
Het |
| Bcar3 |
G |
T |
3: 122,220,225 (GRCm39) |
A41S |
probably benign |
Het |
| Btbd6 |
A |
G |
12: 112,940,932 (GRCm39) |
|
probably benign |
Het |
| Cchcr1 |
A |
G |
17: 35,835,600 (GRCm39) |
T318A |
possibly damaging |
Het |
| Celsr1 |
A |
T |
15: 85,809,719 (GRCm39) |
I2221N |
probably damaging |
Het |
| Cept1 |
C |
T |
3: 106,440,761 (GRCm39) |
W48* |
probably null |
Het |
| Cfap161 |
T |
A |
7: 83,442,484 (GRCm39) |
I85L |
probably benign |
Het |
| Clasp1 |
A |
T |
1: 118,439,910 (GRCm39) |
R640* |
probably null |
Het |
| Col5a1 |
T |
A |
2: 27,842,448 (GRCm39) |
I441N |
unknown |
Het |
| Dnah2 |
T |
C |
11: 69,406,836 (GRCm39) |
D223G |
probably benign |
Het |
| Dnah8 |
G |
A |
17: 30,967,542 (GRCm39) |
D2585N |
probably benign |
Het |
| Dpy19l1 |
A |
T |
9: 24,361,992 (GRCm39) |
M129K |
possibly damaging |
Het |
| Ecpas |
A |
T |
4: 58,810,785 (GRCm39) |
I1524N |
probably damaging |
Het |
| Fcgbpl1 |
C |
G |
7: 27,854,798 (GRCm39) |
P1808R |
probably damaging |
Het |
| Fcrl1 |
C |
A |
3: 87,296,946 (GRCm39) |
H318Q |
probably benign |
Het |
| Fer1l5 |
A |
G |
1: 36,441,612 (GRCm39) |
N609S |
probably damaging |
Het |
| Fkbp4 |
C |
T |
6: 128,410,194 (GRCm39) |
E256K |
probably damaging |
Het |
| Fsip2 |
A |
G |
2: 82,820,430 (GRCm39) |
T5388A |
possibly damaging |
Het |
| Glrx |
G |
A |
13: 75,995,418 (GRCm39) |
|
probably null |
Het |
| Gm7356 |
A |
T |
17: 14,221,726 (GRCm39) |
M101K |
probably damaging |
Het |
| Gstp2 |
A |
T |
19: 4,090,499 (GRCm39) |
I162N |
probably benign |
Het |
| Hectd3 |
A |
C |
4: 116,856,783 (GRCm39) |
K443N |
probably damaging |
Het |
| Hmcn1 |
T |
A |
1: 150,540,535 (GRCm39) |
R2925W |
probably damaging |
Het |
| Hspa1a |
G |
T |
17: 35,189,282 (GRCm39) |
N540K |
probably damaging |
Het |
| Ints6 |
A |
T |
14: 62,938,235 (GRCm39) |
M649K |
probably benign |
Het |
| Katnb1 |
T |
C |
8: 95,822,084 (GRCm39) |
V270A |
possibly damaging |
Het |
| Kctd3 |
A |
G |
1: 188,704,561 (GRCm39) |
S737P |
probably benign |
Het |
| Klra10 |
T |
C |
6: 130,249,507 (GRCm39) |
|
probably null |
Het |
| Lmtk3 |
A |
G |
7: 45,448,013 (GRCm39) |
D1353G |
unknown |
Het |
| Lrrk1 |
A |
G |
7: 65,912,481 (GRCm39) |
V1693A |
probably damaging |
Het |
| Mpnd |
A |
T |
17: 56,316,575 (GRCm39) |
I85F |
probably damaging |
Het |
| Myo3b |
A |
G |
2: 70,179,304 (GRCm39) |
T1173A |
probably benign |
Het |
| Myof |
G |
A |
19: 37,892,279 (GRCm39) |
P1158L |
probably damaging |
Het |
| Naip2 |
A |
C |
13: 100,298,549 (GRCm39) |
S496A |
probably benign |
Het |
| Ncor2 |
A |
G |
5: 125,187,069 (GRCm39) |
|
probably benign |
Het |
| Npepps |
C |
T |
11: 97,149,099 (GRCm39) |
|
probably null |
Het |
| Opn5 |
T |
A |
17: 42,891,640 (GRCm39) |
I266F |
probably benign |
Het |
| Or4a74 |
T |
G |
2: 89,439,790 (GRCm39) |
I219L |
probably damaging |
Het |
| P2rx4 |
A |
G |
5: 122,845,763 (GRCm39) |
D16G |
probably damaging |
Het |
| Padi2 |
G |
T |
4: 140,644,948 (GRCm39) |
V61L |
probably benign |
Het |
| Pkd1l1 |
G |
A |
11: 8,813,911 (GRCm39) |
T1480I |
probably benign |
Het |
| Plcb1 |
T |
C |
2: 135,177,371 (GRCm39) |
S568P |
probably damaging |
Het |
| Rassf10 |
A |
G |
7: 112,554,914 (GRCm39) |
E505G |
probably damaging |
Het |
| Rcan2 |
A |
G |
17: 44,147,225 (GRCm39) |
E21G |
probably benign |
Het |
| Rhob |
G |
T |
12: 8,549,585 (GRCm39) |
C16* |
probably null |
Het |
| Ryr3 |
T |
C |
2: 112,490,413 (GRCm39) |
N3807S |
probably damaging |
Het |
| Sass6 |
T |
A |
3: 116,415,046 (GRCm39) |
N519K |
probably benign |
Het |
| Slco1a8 |
A |
T |
6: 141,939,368 (GRCm39) |
N208K |
possibly damaging |
Het |
| Smad9 |
A |
T |
3: 54,689,864 (GRCm39) |
D28V |
probably damaging |
Het |
| Spmip8 |
A |
T |
8: 96,047,894 (GRCm39) |
|
probably null |
Het |
| Tex14 |
G |
T |
11: 87,405,199 (GRCm39) |
G704C |
probably benign |
Het |
| Tmc3 |
A |
G |
7: 83,271,524 (GRCm39) |
N892S |
probably benign |
Het |
| Tnfaip2 |
T |
A |
12: 111,412,097 (GRCm39) |
L166Q |
probably damaging |
Het |
| Triml2 |
A |
G |
8: 43,638,165 (GRCm39) |
|
probably null |
Het |
| Trio |
A |
G |
15: 27,856,193 (GRCm39) |
V666A |
probably benign |
Het |
| Tshz2 |
G |
T |
2: 169,726,584 (GRCm39) |
L393F |
probably damaging |
Het |
| Ttn |
T |
G |
2: 76,672,115 (GRCm39) |
|
probably benign |
Het |
| Tubb5 |
A |
G |
17: 36,146,734 (GRCm39) |
Y159H |
probably damaging |
Het |
| Umodl1 |
A |
G |
17: 31,178,129 (GRCm39) |
Y35C |
probably damaging |
Het |
| Utp4 |
T |
C |
8: 107,631,078 (GRCm39) |
|
probably null |
Het |
| Vmn1r60 |
A |
T |
7: 5,547,864 (GRCm39) |
C79S |
probably damaging |
Het |
| Wnt5b |
T |
C |
6: 119,410,751 (GRCm39) |
T230A |
probably damaging |
Het |
| Zfp618 |
A |
T |
4: 63,050,943 (GRCm39) |
I575F |
probably damaging |
Het |
| Zmym6 |
G |
T |
4: 127,017,176 (GRCm39) |
V894L |
possibly damaging |
Het |
| Zpbp |
T |
C |
11: 11,412,318 (GRCm39) |
|
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 |
|
|
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 |
|
|
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'- TTCATACAAGGGACTGGATGGG -3'
(R):5'- GTCATTGCACACACTATATCCATTG -3'
Sequencing Primer
(F):5'- CTGGATGGGAGTCTCCAAAC -3'
(R):5'- GCACACACTATATCCATTGTATACAC -3'
|
| Posted On |
2018-05-21 |
Incidental Mutation