Incidental Mutation 'R8878:Col9a1'
| ID |
676664 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
068746-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.092)
|
| Stock # |
R8878 (G1)
|
| Quality Score |
225.009 |
|
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 24236048 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000051579
(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 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: 99.9%
- 10x: 99.7%
- 20x: 98.9%
|
| Validation Efficiency |
99% (73/74) |
| 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: 75 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acss2 |
C |
A |
2: 155,398,324 (GRCm39) |
H348Q |
probably benign |
Het |
| Ago1 |
T |
A |
4: 126,357,516 (GRCm39) |
Y53F |
probably benign |
Het |
| Arrdc5 |
A |
G |
17: 56,601,342 (GRCm39) |
L261P |
probably benign |
Het |
| Asb2 |
C |
A |
12: 103,290,138 (GRCm39) |
W551L |
possibly damaging |
Het |
| Atl2 |
T |
C |
17: 80,160,232 (GRCm39) |
I452V |
probably benign |
Het |
| Atxn7l3 |
T |
C |
11: 102,183,545 (GRCm39) |
S203G |
probably benign |
Het |
| Bche |
A |
G |
3: 73,608,506 (GRCm39) |
F307L |
probably benign |
Het |
| C6 |
T |
C |
15: 4,826,454 (GRCm39) |
V679A |
probably benign |
Het |
| Cd163 |
A |
T |
6: 124,297,469 (GRCm39) |
N872Y |
probably damaging |
Het |
| Cdkal1 |
C |
A |
13: 29,658,607 (GRCm39) |
V380F |
probably damaging |
Het |
| Ceacam11 |
A |
T |
7: 17,709,536 (GRCm39) |
I245L |
probably benign |
Het |
| Ceacam16 |
G |
T |
7: 19,592,656 (GRCm39) |
T84K |
possibly damaging |
Het |
| Ceacam2 |
T |
A |
7: 25,227,351 (GRCm39) |
Q172L |
probably benign |
Het |
| Chga |
T |
G |
12: 102,527,720 (GRCm39) |
S125A |
possibly damaging |
Het |
| Crybg3 |
C |
A |
16: 59,380,547 (GRCm39) |
A236S |
probably benign |
Het |
| Csmd1 |
A |
G |
8: 15,960,528 (GRCm39) |
Y3296H |
probably damaging |
Het |
| Cyp2j8 |
C |
A |
4: 96,358,807 (GRCm39) |
V371L |
possibly damaging |
Het |
| Des |
C |
A |
1: 75,337,137 (GRCm39) |
L26M |
unknown |
Het |
| Edc3 |
A |
G |
9: 57,623,484 (GRCm39) |
S140G |
possibly damaging |
Het |
| Fam161a |
C |
T |
11: 22,970,092 (GRCm39) |
T90I |
probably benign |
Het |
| Fancm |
T |
C |
12: 65,173,522 (GRCm39) |
Y1945H |
probably damaging |
Het |
| Fbn2 |
C |
T |
18: 58,257,318 (GRCm39) |
V350I |
probably benign |
Het |
| Git2 |
A |
G |
5: 114,899,649 (GRCm39) |
C235R |
possibly damaging |
Het |
| Gk2 |
T |
C |
5: 97,604,341 (GRCm39) |
K166E |
probably benign |
Het |
| Gm12258 |
G |
A |
11: 58,750,112 (GRCm39) |
R429H |
unknown |
Het |
| Gm7247 |
T |
G |
14: 51,666,210 (GRCm39) |
|
probably benign |
Het |
| Gmppa |
A |
G |
1: 75,414,932 (GRCm39) |
Y59C |
probably damaging |
Het |
| Has1 |
G |
T |
17: 18,070,321 (GRCm39) |
A200E |
possibly damaging |
Het |
| Hbs1l |
T |
C |
10: 21,234,711 (GRCm39) |
I588T |
possibly damaging |
Het |
| Helz2 |
A |
G |
2: 180,874,560 (GRCm39) |
V1978A |
possibly damaging |
Het |
| Hoxb9 |
T |
C |
11: 96,165,557 (GRCm39) |
Y209H |
probably damaging |
Het |
| Hps5 |
T |
C |
7: 46,421,345 (GRCm39) |
D706G |
probably benign |
Het |
| Hydin |
T |
C |
8: 111,035,720 (GRCm39) |
V137A |
probably benign |
Het |
| Ifngr2 |
T |
C |
16: 91,359,847 (GRCm39) |
I318T |
probably benign |
Het |
| Iqgap3 |
C |
T |
3: 88,020,532 (GRCm39) |
T1290I |
probably damaging |
Het |
| Jrk |
A |
T |
15: 74,578,988 (GRCm39) |
V99E |
probably benign |
Het |
| Kalrn |
G |
A |
16: 34,025,696 (GRCm39) |
T931M |
probably damaging |
Het |
| Kalrn |
G |
A |
16: 34,018,830 (GRCm39) |
P1311S |
probably benign |
Het |
| Kirrel3 |
A |
G |
9: 34,850,561 (GRCm39) |
|
probably benign |
Het |
| Klk1b9 |
T |
C |
7: 43,443,782 (GRCm39) |
F99L |
possibly damaging |
Het |
| Lamb3 |
T |
C |
1: 193,013,124 (GRCm39) |
C450R |
probably damaging |
Het |
| Lyst |
T |
A |
13: 13,815,661 (GRCm39) |
S1182T |
probably benign |
Het |
| Map1a |
T |
C |
2: 121,138,125 (GRCm39) |
V2933A |
probably damaging |
Het |
| Map2k5 |
A |
T |
9: 63,250,667 (GRCm39) |
|
probably null |
Het |
| Mcm6 |
A |
G |
1: 128,283,248 (GRCm39) |
|
probably null |
Het |
| Mmp17 |
G |
A |
5: 129,683,378 (GRCm39) |
V505M |
probably damaging |
Het |
| Mpped2 |
A |
G |
2: 106,575,065 (GRCm39) |
D50G |
probably damaging |
Het |
| Mtf1 |
T |
A |
4: 124,715,023 (GRCm39) |
L216* |
probably null |
Het |
| Niban2 |
A |
T |
2: 32,811,105 (GRCm39) |
M372L |
probably benign |
Het |
| Obscn |
T |
C |
11: 58,890,638 (GRCm39) |
E7298G |
unknown |
Het |
| Or52ab7 |
A |
T |
7: 102,978,212 (GRCm39) |
H173L |
possibly damaging |
Het |
| Or56a3 |
T |
C |
7: 104,735,763 (GRCm39) |
L280P |
probably damaging |
Het |
| Or6c205 |
T |
C |
10: 129,086,883 (GRCm39) |
L160P |
probably benign |
Het |
| Or7d9 |
A |
G |
9: 20,197,358 (GRCm39) |
D129G |
probably damaging |
Het |
| Otulinl |
T |
A |
15: 27,664,884 (GRCm39) |
H24L |
probably benign |
Het |
| Pax2 |
G |
A |
19: 44,777,215 (GRCm39) |
|
probably null |
Het |
| Pcnt |
T |
A |
10: 76,244,675 (GRCm39) |
E1135V |
probably damaging |
Het |
| Pgap3 |
A |
T |
11: 98,281,924 (GRCm39) |
V129D |
probably benign |
Het |
| Polq |
A |
G |
16: 36,860,869 (GRCm39) |
N497S |
probably benign |
Het |
| Ppfia4 |
T |
C |
1: 134,227,122 (GRCm39) |
T1138A |
|
Het |
| Prickle4 |
A |
G |
17: 48,001,587 (GRCm39) |
L32P |
|
Het |
| Prl2c2 |
C |
T |
13: 13,171,896 (GRCm39) |
G158R |
probably damaging |
Het |
| Psd3 |
A |
G |
8: 68,210,750 (GRCm39) |
I752T |
probably benign |
Het |
| Sag |
A |
T |
1: 87,756,158 (GRCm39) |
Y255F |
probably benign |
Het |
| Scn7a |
A |
T |
2: 66,506,199 (GRCm39) |
D1563E |
probably damaging |
Het |
| Secisbp2 |
A |
G |
13: 51,837,404 (GRCm39) |
N855S |
probably benign |
Het |
| Setd2 |
T |
C |
9: 110,421,467 (GRCm39) |
V2011A |
probably benign |
Het |
| Slc30a6 |
T |
C |
17: 74,730,112 (GRCm39) |
V334A |
probably damaging |
Het |
| Spen |
A |
G |
4: 141,204,520 (GRCm39) |
V1369A |
unknown |
Het |
| Stac2 |
T |
C |
11: 97,932,373 (GRCm39) |
T207A |
probably benign |
Het |
| Syne2 |
T |
C |
12: 75,952,067 (GRCm39) |
V445A |
probably benign |
Het |
| Tas2r131 |
C |
A |
6: 132,934,467 (GRCm39) |
W114L |
probably damaging |
Het |
| Tgfbrap1 |
G |
A |
1: 43,088,959 (GRCm39) |
R815* |
probably null |
Het |
| Trpv2 |
A |
T |
11: 62,481,112 (GRCm39) |
I404L |
probably benign |
Het |
| Zfp236 |
G |
A |
18: 82,617,122 (GRCm39) |
T1791M |
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 |
|
|
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 |
|
|
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'- CCACCATAGAGAGGCATCCTTG -3'
(R):5'- AAGTTGCTGCCCCAAGGATC -3'
Sequencing Primer
(F):5'- GCATCCTTGCTGGTGTGTG -3'
(R):5'- ACGGGTACAAAACTAGTCTCTTCTC -3'
|
| Posted On |
2021-07-15 |
Incidental Mutation