Incidental Mutation 'R9205:Col9a1'
| ID |
698412 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.092)
|
| Stock # |
R9205 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to G
at 24224175 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Arginine
at position 119
(M119R)
|
| 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: M119R
|
| SMART Domains |
Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: M119R
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.3%
|
| Validation Efficiency |
95% (76/80) |
| 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: 79 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aebp2 |
T |
A |
6: 140,587,954 (GRCm39) |
H341Q |
probably damaging |
Het |
| Apob |
G |
A |
12: 8,030,635 (GRCm39) |
A125T |
probably damaging |
Het |
| Bace2 |
G |
T |
16: 97,158,059 (GRCm39) |
A20S |
unknown |
Het |
| Bcar1 |
T |
C |
8: 112,442,341 (GRCm39) |
Y238C |
probably damaging |
Het |
| Brinp3 |
A |
T |
1: 146,777,827 (GRCm39) |
D758V |
possibly damaging |
Het |
| Btnl10 |
T |
C |
11: 58,811,345 (GRCm39) |
S223P |
probably damaging |
Het |
| Cckar |
C |
T |
5: 53,864,587 (GRCm39) |
|
probably null |
Het |
| Cdhr2 |
A |
G |
13: 54,861,801 (GRCm39) |
N66S |
probably benign |
Het |
| Chd9 |
A |
G |
8: 91,757,270 (GRCm39) |
M1890V |
probably benign |
Het |
| Col6a5 |
C |
T |
9: 105,755,837 (GRCm39) |
G2196R |
probably damaging |
Het |
| Cryaa |
A |
G |
17: 31,898,642 (GRCm39) |
H123R |
probably damaging |
Het |
| Cux1 |
A |
T |
5: 136,398,989 (GRCm39) |
D171E |
probably damaging |
Het |
| Dgkz |
T |
A |
2: 91,764,144 (GRCm39) |
T1067S |
probably benign |
Het |
| Dnah11 |
C |
T |
12: 117,991,251 (GRCm39) |
E2372K |
probably damaging |
Het |
| Dnah5 |
T |
C |
15: 28,448,480 (GRCm39) |
M4181T |
possibly damaging |
Het |
| Dnajb14 |
A |
G |
3: 137,614,145 (GRCm39) |
E352G |
possibly damaging |
Het |
| Dnmt3l |
T |
A |
10: 77,892,586 (GRCm39) |
|
probably null |
Het |
| Dph6 |
T |
C |
2: 114,399,995 (GRCm39) |
I117V |
probably damaging |
Het |
| Dsg1a |
A |
G |
18: 20,473,228 (GRCm39) |
D767G |
probably damaging |
Het |
| Edn3 |
C |
T |
2: 174,603,482 (GRCm39) |
P77S |
possibly damaging |
Het |
| Fbln7 |
A |
C |
2: 128,737,168 (GRCm39) |
S328R |
probably null |
Het |
| Fbn2 |
T |
C |
18: 58,192,428 (GRCm39) |
R1518G |
probably damaging |
Het |
| Foxi2 |
A |
T |
7: 135,013,525 (GRCm39) |
T252S |
probably benign |
Het |
| Foxred2 |
A |
G |
15: 77,836,206 (GRCm39) |
S384P |
probably damaging |
Het |
| Gdpd1 |
G |
A |
11: 86,936,009 (GRCm39) |
H174Y |
probably benign |
Het |
| Gm10542 |
A |
C |
18: 44,337,705 (GRCm39) |
D61A |
possibly damaging |
Het |
| Gm10563 |
TTCCTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCCTC |
TTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCCTC |
4: 155,720,307 (GRCm39) |
|
probably benign |
Het |
| H2-Ab1 |
A |
G |
17: 34,483,981 (GRCm39) |
E114G |
probably damaging |
Het |
| Htt |
C |
T |
5: 34,976,367 (GRCm39) |
T723M |
probably benign |
Het |
| Igfn1 |
C |
T |
1: 135,903,695 (GRCm39) |
V348I |
probably damaging |
Het |
| Itpr1 |
T |
A |
6: 108,466,810 (GRCm39) |
L2173Q |
probably damaging |
Het |
| Lamp5 |
A |
G |
2: 135,901,521 (GRCm39) |
Y115C |
probably damaging |
Het |
| Lrp1 |
T |
A |
10: 127,430,850 (GRCm39) |
K400* |
probably null |
Het |
| Man2a2 |
C |
T |
7: 80,010,868 (GRCm39) |
V708I |
probably benign |
Het |
| Matr3 |
T |
C |
18: 35,720,774 (GRCm39) |
S746P |
probably benign |
Het |
| Me1 |
C |
T |
9: 86,480,847 (GRCm39) |
V353M |
probably benign |
Het |
| Mideas |
A |
C |
12: 84,199,661 (GRCm39) |
F1020V |
probably benign |
Het |
| Nbeal1 |
T |
A |
1: 60,317,839 (GRCm39) |
D1925E |
probably damaging |
Het |
| Oca2 |
T |
A |
7: 55,966,168 (GRCm39) |
F387I |
probably damaging |
Het |
| Opn3 |
G |
T |
1: 175,490,655 (GRCm39) |
N335K |
probably benign |
Het |
| Or5d36 |
T |
A |
2: 87,900,778 (GRCm39) |
H316L |
probably benign |
Het |
| Or5k17 |
T |
G |
16: 58,746,485 (GRCm39) |
I150L |
probably benign |
Het |
| Or5k17 |
G |
T |
16: 58,746,486 (GRCm39) |
F149L |
probably benign |
Het |
| Or6d12 |
T |
A |
6: 116,493,315 (GRCm39) |
N192K |
probably benign |
Het |
| Or6k2 |
T |
C |
1: 173,986,456 (GRCm39) |
I39T |
probably benign |
Het |
| Or8b48 |
T |
A |
9: 38,493,373 (GRCm39) |
S267T |
probably benign |
Het |
| Osm |
A |
G |
11: 4,188,504 (GRCm39) |
N44D |
possibly damaging |
Het |
| Otop2 |
T |
C |
11: 115,219,912 (GRCm39) |
Y251H |
probably damaging |
Het |
| Pappa |
T |
C |
4: 65,074,612 (GRCm39) |
S389P |
possibly damaging |
Het |
| Polr1d |
C |
T |
5: 147,038,068 (GRCm39) |
A19V |
probably damaging |
Het |
| Ptchd4 |
G |
A |
17: 42,814,276 (GRCm39) |
V726M |
probably benign |
Het |
| Pzp |
T |
A |
6: 128,473,626 (GRCm39) |
D731V |
probably benign |
Het |
| Rgl2 |
A |
T |
17: 34,155,002 (GRCm39) |
I669F |
probably damaging |
Het |
| Rpl38 |
T |
C |
11: 114,563,114 (GRCm39) |
*71R |
probably null |
Het |
| Rufy1 |
G |
A |
11: 50,289,301 (GRCm39) |
R514W |
probably damaging |
Het |
| Ruvbl2 |
G |
A |
7: 45,083,741 (GRCm39) |
|
probably benign |
Het |
| Scn9a |
T |
G |
2: 66,363,657 (GRCm39) |
I874L |
probably damaging |
Het |
| Slc14a2 |
A |
G |
18: 78,238,951 (GRCm39) |
S85P |
probably benign |
Het |
| Slc17a1 |
A |
G |
13: 24,062,794 (GRCm39) |
I287V |
probably benign |
Het |
| Slc35f3 |
T |
A |
8: 127,115,928 (GRCm39) |
I285N |
probably damaging |
Het |
| Slx4 |
A |
G |
16: 3,805,927 (GRCm39) |
S542P |
possibly damaging |
Het |
| Sox30 |
A |
T |
11: 45,908,180 (GRCm39) |
L782F |
probably damaging |
Het |
| Sspo |
A |
G |
6: 48,432,806 (GRCm39) |
N894S |
probably benign |
Het |
| Syne1 |
G |
A |
10: 5,152,013 (GRCm39) |
Q5765* |
probably null |
Het |
| Taar7e |
T |
C |
10: 23,913,972 (GRCm39) |
I154T |
probably benign |
Het |
| Tars1 |
A |
G |
15: 11,397,265 (GRCm39) |
|
probably null |
Het |
| Thap1 |
CAGCATCTGCTCGGAGCA |
CAGCA |
8: 26,650,884 (GRCm39) |
|
probably null |
Het |
| Tmem198b |
A |
T |
10: 128,639,057 (GRCm39) |
C29S |
probably damaging |
Het |
| Tnr |
A |
C |
1: 159,722,617 (GRCm39) |
M1021L |
probably benign |
Het |
| Tom1l1 |
G |
A |
11: 90,548,644 (GRCm39) |
P309L |
probably damaging |
Het |
| Traf4 |
A |
G |
11: 78,051,927 (GRCm39) |
S186P |
probably benign |
Het |
| Trpm1 |
T |
G |
7: 63,890,319 (GRCm39) |
V974G |
possibly damaging |
Het |
| Tsga10 |
T |
A |
1: 37,880,359 (GRCm39) |
|
probably benign |
Het |
| Tyw1 |
G |
A |
5: 130,298,065 (GRCm39) |
R202Q |
probably damaging |
Het |
| Vmn2r93 |
A |
T |
17: 18,524,281 (GRCm39) |
I92F |
probably damaging |
Het |
| Zfp457 |
A |
T |
13: 67,441,965 (GRCm39) |
D203E |
probably benign |
Het |
| Zfp518b |
G |
A |
5: 38,831,501 (GRCm39) |
S168F |
probably damaging |
Het |
| Zfp7 |
TGCGGGAAAGGTTTCCACCTGAGCG |
TGCG |
15: 76,774,800 (GRCm39) |
|
probably benign |
Het |
| Zfp777 |
G |
A |
6: 48,002,521 (GRCm39) |
T523M |
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 |
|
|
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 |
|
|
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'- ACACTGTAGCCTTTCCGCAG -3'
(R):5'- AAAAGAGTGGCGCTTGTTCTTTC -3'
Sequencing Primer
(F):5'- CCGCAGGACTAGAATTCAAA -3'
(R):5'- ATCATGAGCTTATGCCACCGG -3'
|
| Posted On |
2022-02-07 |
Incidental Mutation