Incidental Mutation 'R8795:Col9a1'
| ID |
671158 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
068636-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.121)
|
| Stock # |
R8795 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 24233812 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Glycine
at position 249
(R249G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000051579
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000054588]
[ENSMUST00000088349]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
unknown
Transcript: ENSMUST00000054588
AA Change: R249G
|
| SMART Domains |
Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: R249G
| 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
|
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.0%
|
| Validation Efficiency |
97% (72/74) |
| 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: 74 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aars2 |
A |
T |
17: 45,818,598 (GRCm39) |
M128L |
probably damaging |
Het |
| Abcc12 |
A |
G |
8: 87,258,213 (GRCm39) |
S768P |
possibly damaging |
Het |
| Adamts8 |
A |
T |
9: 30,854,484 (GRCm39) |
M118L |
probably benign |
Het |
| Adgrl4 |
A |
G |
3: 151,216,416 (GRCm39) |
N533S |
probably benign |
Het |
| Agk |
T |
G |
6: 40,363,854 (GRCm39) |
I278R |
possibly damaging |
Het |
| Atr |
T |
A |
9: 95,749,584 (GRCm39) |
W466R |
probably damaging |
Het |
| Cacna1h |
C |
T |
17: 25,612,538 (GRCm39) |
V387I |
probably damaging |
Het |
| Cand2 |
T |
G |
6: 115,763,889 (GRCm39) |
D270E |
probably benign |
Het |
| Ccdc107 |
C |
T |
4: 43,495,514 (GRCm39) |
T139M |
probably damaging |
Het |
| Cenpl |
A |
G |
1: 160,910,584 (GRCm39) |
E177G |
probably benign |
Het |
| Clint1 |
C |
A |
11: 45,775,178 (GRCm39) |
Q56K |
probably damaging |
Het |
| Cpne5 |
C |
T |
17: 29,423,662 (GRCm39) |
|
probably benign |
Het |
| Ddx27 |
A |
G |
2: 166,859,730 (GRCm39) |
D54G |
probably benign |
Het |
| Dync2h1 |
C |
T |
9: 7,137,087 (GRCm39) |
E1468K |
probably benign |
Het |
| E130308A19Rik |
A |
T |
4: 59,737,676 (GRCm39) |
N429I |
possibly damaging |
Het |
| Endov |
G |
T |
11: 119,390,380 (GRCm39) |
G86C |
possibly damaging |
Het |
| Ercc5 |
A |
T |
1: 44,203,089 (GRCm39) |
Y242F |
possibly damaging |
Het |
| Gabrr1 |
T |
A |
4: 33,161,756 (GRCm39) |
V360E |
probably damaging |
Het |
| Gcn1 |
T |
C |
5: 115,752,454 (GRCm39) |
I2153T |
probably benign |
Het |
| Gje1 |
T |
C |
10: 14,593,870 (GRCm39) |
N8S |
probably benign |
Het |
| Greb1l |
A |
G |
18: 10,553,739 (GRCm39) |
H1580R |
probably damaging |
Het |
| Grin1 |
C |
G |
2: 25,187,468 (GRCm39) |
S614T |
probably damaging |
Het |
| Hmcn2 |
A |
G |
2: 31,315,393 (GRCm39) |
N3714S |
probably benign |
Het |
| Idh1 |
CA |
CAA |
1: 65,204,347 (GRCm39) |
|
probably null |
Het |
| Ifitm2 |
A |
T |
7: 140,535,661 (GRCm39) |
H56Q |
probably damaging |
Het |
| Ifrd1 |
G |
A |
12: 40,263,076 (GRCm39) |
T218I |
possibly damaging |
Het |
| Igkv1-99 |
G |
T |
6: 68,519,370 (GRCm39) |
G109V |
|
Het |
| Impg2 |
A |
G |
16: 56,080,611 (GRCm39) |
E805G |
probably benign |
Het |
| Itgb6 |
T |
A |
2: 60,483,629 (GRCm39) |
N260Y |
probably damaging |
Het |
| Maneal |
G |
T |
4: 124,750,483 (GRCm39) |
Y424* |
probably null |
Het |
| Map4k2 |
T |
G |
19: 6,401,640 (GRCm39) |
C677W |
probably damaging |
Het |
| Med6 |
T |
C |
12: 81,638,034 (GRCm39) |
H59R |
probably benign |
Het |
| Mms22l |
T |
A |
4: 24,536,245 (GRCm39) |
D571E |
probably benign |
Het |
| Mroh8 |
A |
G |
2: 157,067,493 (GRCm39) |
F622S |
probably damaging |
Het |
| Mrpl44 |
A |
T |
1: 79,753,974 (GRCm39) |
Q42L |
probably damaging |
Het |
| Myh8 |
G |
T |
11: 67,174,203 (GRCm39) |
|
probably benign |
Het |
| Ndufb2 |
T |
C |
6: 39,569,586 (GRCm39) |
V13A |
probably benign |
Het |
| Nf1 |
T |
A |
11: 79,316,442 (GRCm39) |
L499Q |
probably damaging |
Het |
| Opa1 |
T |
C |
16: 29,448,450 (GRCm39) |
C874R |
probably damaging |
Het |
| Or1i2 |
T |
C |
10: 78,447,698 (GRCm39) |
Y259C |
probably damaging |
Het |
| Or4c99 |
T |
G |
2: 88,329,855 (GRCm39) |
V142G |
probably damaging |
Het |
| Or4k37 |
T |
A |
2: 111,158,881 (GRCm39) |
L39* |
probably null |
Het |
| Or6c6 |
T |
C |
10: 129,187,194 (GRCm39) |
I254T |
probably damaging |
Het |
| Pld3 |
T |
A |
7: 27,235,286 (GRCm39) |
D314V |
possibly damaging |
Het |
| Pou6f1 |
A |
C |
15: 100,485,686 (GRCm39) |
C114W |
possibly damaging |
Het |
| Prl2c1 |
A |
C |
13: 28,033,389 (GRCm39) |
Q2P |
possibly damaging |
Het |
| Prl2c1 |
G |
T |
13: 28,033,390 (GRCm39) |
Q2H |
probably benign |
Het |
| Pzp |
C |
A |
6: 128,471,701 (GRCm39) |
K908N |
probably damaging |
Het |
| Rab6b |
G |
A |
9: 103,039,825 (GRCm39) |
G125D |
probably damaging |
Het |
| Rhbdd2 |
C |
T |
5: 135,663,985 (GRCm39) |
T69I |
probably benign |
Het |
| Samd9l |
A |
T |
6: 3,374,221 (GRCm39) |
Y1013* |
probably null |
Het |
| Slc13a4 |
T |
A |
6: 35,260,230 (GRCm39) |
T217S |
probably benign |
Het |
| Slc66a3 |
A |
G |
12: 17,043,481 (GRCm39) |
W150R |
probably damaging |
Het |
| Smarcad1 |
T |
C |
6: 65,049,033 (GRCm39) |
L253S |
probably benign |
Het |
| Snrpa |
C |
A |
7: 26,891,034 (GRCm39) |
V146L |
possibly damaging |
Het |
| Spata31f1e |
A |
G |
4: 42,792,992 (GRCm39) |
V380A |
probably benign |
Het |
| Srrt |
A |
T |
5: 137,298,238 (GRCm39) |
D311E |
probably benign |
Het |
| Stk32b |
A |
T |
5: 37,806,483 (GRCm39) |
F20L |
probably damaging |
Het |
| Sult2a7 |
T |
C |
7: 14,224,014 (GRCm39) |
T136A |
probably benign |
Het |
| Sv2a |
G |
A |
3: 96,094,396 (GRCm39) |
V244I |
probably benign |
Het |
| Tesk1 |
T |
A |
4: 43,446,070 (GRCm39) |
|
probably null |
Het |
| Tmem260 |
A |
G |
14: 48,689,370 (GRCm39) |
H63R |
probably damaging |
Het |
| Ugt1a6b |
A |
G |
1: 88,034,794 (GRCm39) |
E44G |
probably benign |
Het |
| Unc79 |
A |
T |
12: 103,074,513 (GRCm39) |
I1363F |
probably damaging |
Het |
| Usp15 |
T |
A |
10: 122,988,953 (GRCm39) |
N255Y |
probably benign |
Het |
| Usp35 |
A |
G |
7: 96,961,167 (GRCm39) |
V753A |
possibly damaging |
Het |
| Usp35 |
T |
C |
7: 96,961,270 (GRCm39) |
N719D |
probably benign |
Het |
| Vmn2r104 |
T |
A |
17: 20,262,988 (GRCm39) |
I158L |
probably benign |
Het |
| Vmn2r69 |
A |
T |
7: 85,064,883 (GRCm39) |
M1K |
probably null |
Het |
| Zan |
C |
T |
5: 137,396,522 (GRCm39) |
E4345K |
unknown |
Het |
| Zc3h7a |
A |
T |
16: 10,965,147 (GRCm39) |
M662K |
possibly damaging |
Het |
| Zfp512 |
G |
A |
5: 31,634,134 (GRCm39) |
V438M |
probably damaging |
Het |
| Zfy1 |
T |
C |
Y: 738,945 (GRCm39) |
D87G |
unknown |
Het |
| Zmym4 |
A |
T |
4: 126,799,819 (GRCm39) |
V653E |
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 |
|
|
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 |
|
|
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'- GTCAAGGCTGTGTTTCACTG -3'
(R):5'- TACCAGATACAGGTCTGCCC -3'
Sequencing Primer
(F):5'- CACTGAGCTAAGTTCAAAGGGCTTC -3'
(R):5'- TGAAGGGTCCTACAGCCAAGTC -3'
|
| Posted On |
2021-04-30 |
Incidental Mutation