Incidental Mutation 'R4988:Col9a1'
| ID |
385933 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a1
|
| Ensembl Gene |
ENSMUSG00000026147 |
| Gene Name |
collagen, type IX, alpha 1 |
| Synonyms |
Col9a-1 |
| MMRRC Submission |
042582-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.092)
|
| Stock # |
R4988 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
24216691-24291765 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 24224273 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 152
(S152P)
|
| 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: S152P
|
| SMART Domains |
Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: S152P
| 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 |
0.5055 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 93.7%
|
| Validation Efficiency |
100% (58/58) |
| 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: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| AA986860 |
G |
A |
1: 130,670,447 (GRCm39) |
G223E |
probably damaging |
Het |
| Abcb11 |
T |
C |
2: 69,154,236 (GRCm39) |
N110S |
probably benign |
Het |
| Acaca |
T |
A |
11: 84,154,121 (GRCm39) |
H947Q |
probably damaging |
Het |
| Akap13 |
T |
C |
7: 75,380,276 (GRCm39) |
M2202T |
probably damaging |
Het |
| Amy2b |
T |
C |
3: 113,058,550 (GRCm39) |
|
noncoding transcript |
Het |
| Arhgef4 |
A |
T |
1: 34,762,535 (GRCm39) |
H597L |
unknown |
Het |
| Asgr2 |
A |
G |
11: 69,988,665 (GRCm39) |
I119M |
probably benign |
Het |
| Casc3 |
T |
G |
11: 98,712,700 (GRCm39) |
|
probably null |
Het |
| Cbr1b |
A |
G |
16: 93,426,884 (GRCm39) |
T162A |
probably benign |
Het |
| Ccdc7b |
T |
A |
8: 129,872,013 (GRCm39) |
M239K |
possibly damaging |
Het |
| Cdc27 |
A |
G |
11: 104,416,950 (GRCm39) |
S334P |
possibly damaging |
Het |
| Ces1c |
T |
C |
8: 93,827,336 (GRCm39) |
E476G |
probably damaging |
Het |
| Clec3a |
T |
A |
8: 115,144,827 (GRCm39) |
M1K |
probably null |
Het |
| Cpd |
A |
G |
11: 76,705,656 (GRCm39) |
S359P |
probably damaging |
Het |
| Ctnnal1 |
A |
T |
4: 56,847,854 (GRCm39) |
L95* |
probably null |
Het |
| Dhx57 |
T |
C |
17: 80,558,827 (GRCm39) |
D1044G |
probably damaging |
Het |
| Dync1h1 |
C |
A |
12: 110,624,560 (GRCm39) |
T3700N |
probably damaging |
Het |
| Efcab5 |
A |
G |
11: 77,028,078 (GRCm39) |
S418P |
probably damaging |
Het |
| Elp5 |
T |
C |
11: 69,870,668 (GRCm39) |
D59G |
probably benign |
Het |
| Fam210a |
G |
A |
18: 68,409,218 (GRCm39) |
R31C |
probably benign |
Het |
| Farp1 |
A |
G |
14: 121,513,019 (GRCm39) |
T792A |
probably damaging |
Het |
| Fmc1 |
A |
T |
6: 38,511,917 (GRCm39) |
Y37F |
probably benign |
Het |
| Gm10717 |
T |
A |
9: 3,026,368 (GRCm39) |
L72M |
probably benign |
Het |
| Gm1758 |
A |
T |
16: 14,320,067 (GRCm39) |
|
noncoding transcript |
Het |
| Gm4553 |
G |
A |
7: 141,718,729 (GRCm39) |
|
probably benign |
Het |
| Gpr156 |
A |
G |
16: 37,768,577 (GRCm39) |
T33A |
possibly damaging |
Het |
| Hhat |
A |
T |
1: 192,339,602 (GRCm39) |
|
probably benign |
Het |
| Hint2 |
T |
C |
4: 43,654,953 (GRCm39) |
I59V |
possibly damaging |
Het |
| Hps4 |
C |
T |
5: 112,526,019 (GRCm39) |
|
probably benign |
Het |
| Hsd17b8 |
A |
G |
17: 34,246,262 (GRCm39) |
F137S |
probably damaging |
Het |
| Klrc2 |
A |
T |
6: 129,633,426 (GRCm39) |
C192S |
probably benign |
Het |
| Map1a |
C |
T |
2: 121,133,531 (GRCm39) |
T1211I |
probably benign |
Het |
| Mtus1 |
T |
C |
8: 41,537,578 (GRCm39) |
N46S |
probably benign |
Het |
| Myo18a |
T |
C |
11: 77,736,347 (GRCm39) |
|
probably null |
Het |
| Nbas |
T |
C |
12: 13,458,266 (GRCm39) |
S1258P |
probably benign |
Het |
| Ndst1 |
C |
T |
18: 60,836,005 (GRCm39) |
G426D |
probably damaging |
Het |
| Nepro |
A |
G |
16: 44,554,905 (GRCm39) |
E327G |
possibly damaging |
Het |
| Nutm2 |
C |
T |
13: 50,626,379 (GRCm39) |
T322I |
possibly damaging |
Het |
| Or10s1 |
G |
A |
9: 39,985,961 (GRCm39) |
M123I |
probably damaging |
Het |
| Or1j18 |
T |
C |
2: 36,624,996 (GRCm39) |
I221T |
possibly damaging |
Het |
| Or2m13 |
A |
T |
16: 19,225,860 (GRCm39) |
M302K |
probably benign |
Het |
| Or6c66 |
T |
C |
10: 129,461,930 (GRCm39) |
|
probably null |
Het |
| Pcdhb15 |
G |
A |
18: 37,608,855 (GRCm39) |
A696T |
probably damaging |
Het |
| Polm |
C |
A |
11: 5,787,618 (GRCm39) |
R45L |
probably damaging |
Het |
| Pon3 |
G |
A |
6: 5,254,582 (GRCm39) |
R27* |
probably null |
Het |
| Proser1 |
T |
C |
3: 53,387,046 (GRCm39) |
I845T |
probably damaging |
Het |
| Rassf8 |
A |
G |
6: 145,762,870 (GRCm39) |
N406D |
possibly damaging |
Het |
| Skint10 |
A |
T |
4: 112,586,069 (GRCm39) |
C182* |
probably null |
Het |
| Slc6a19 |
C |
T |
13: 73,833,959 (GRCm39) |
W366* |
probably null |
Het |
| St7 |
T |
C |
6: 17,934,225 (GRCm39) |
F470L |
probably damaging |
Het |
| St8sia4 |
T |
A |
1: 95,519,522 (GRCm39) |
Y322F |
possibly damaging |
Het |
| Trav8n-2 |
A |
T |
14: 53,975,814 (GRCm39) |
|
probably benign |
Het |
| Vwa8 |
A |
T |
14: 79,435,723 (GRCm39) |
H1811L |
probably benign |
Het |
| Zfp14 |
G |
A |
7: 29,737,482 (GRCm39) |
T501I |
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 |
|
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'- ACACTGTAGCCTTTCCGCAG -3'
(R):5'- AGCCATCCGCATCAATCTGG -3'
Sequencing Primer
(F):5'- AGCACACACACAGAAAAATGG -3'
(R):5'- GCATCAATCTGGCCTCTTGG -3'
|
| Posted On |
2016-05-10 |
Incidental Mutation