Incidental Mutation 'R5434:Col9a2'
ID |
484572 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col9a2
|
Ensembl Gene |
ENSMUSG00000028626 |
Gene Name |
collagen, type IX, alpha 2 |
Synonyms |
Col9a-2 |
MMRRC Submission |
042999-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R5434 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
4 |
Chromosomal Location |
120896763-120912522 bp(+) (GRCm39) |
Type of Mutation |
nonsense |
DNA Base Change (assembly) |
A to T
at 120898162 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Arginine to Stop codon
at position 25
(R25*)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000030372
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030372]
|
AlphaFold |
no structure available at present |
Predicted Effect |
probably null
Transcript: ENSMUST00000030372
AA Change: R25*
|
SMART Domains |
Protein: ENSMUSP00000030372 Gene: ENSMUSG00000028626 AA Change: R25*
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
22 |
N/A |
INTRINSIC |
Pfam:Collagen
|
24 |
82 |
7.3e-12 |
PFAM |
Pfam:Collagen
|
59 |
115 |
2.4e-10 |
PFAM |
Pfam:Collagen
|
113 |
170 |
2e-8 |
PFAM |
Pfam:Collagen
|
176 |
236 |
8.9e-11 |
PFAM |
low complexity region
|
258 |
277 |
N/A |
INTRINSIC |
low complexity region
|
288 |
315 |
N/A |
INTRINSIC |
Pfam:Collagen
|
357 |
435 |
4.4e-8 |
PFAM |
Pfam:Collagen
|
459 |
523 |
6.1e-11 |
PFAM |
Pfam:Collagen
|
548 |
610 |
4.5e-11 |
PFAM |
low complexity region
|
639 |
661 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151987
|
Meta Mutation Damage Score |
0.9755 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.6%
|
Validation Efficiency |
100% (57/57) |
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, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 55 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Angptl6 |
G |
T |
9: 20,786,821 (GRCm39) |
Q301K |
probably damaging |
Het |
Ankfn1 |
T |
C |
11: 89,344,013 (GRCm39) |
Y323C |
probably damaging |
Het |
Arid5b |
T |
A |
10: 67,932,719 (GRCm39) |
H818L |
possibly damaging |
Het |
Atg13 |
G |
T |
2: 91,515,110 (GRCm39) |
|
probably null |
Het |
Bltp1 |
A |
C |
3: 36,929,665 (GRCm39) |
D94A |
probably damaging |
Het |
Bop1 |
T |
C |
15: 76,339,611 (GRCm39) |
M245V |
probably benign |
Het |
Ces2a |
T |
A |
8: 105,464,041 (GRCm39) |
F224L |
probably damaging |
Het |
Cntnap5b |
A |
G |
1: 99,999,926 (GRCm39) |
H228R |
probably benign |
Het |
Dcaf12 |
G |
T |
4: 41,302,744 (GRCm39) |
T137N |
probably benign |
Het |
Dennd4c |
A |
G |
4: 86,729,693 (GRCm39) |
N765S |
probably benign |
Het |
Dnah12 |
A |
G |
14: 26,581,256 (GRCm39) |
Y3162C |
probably damaging |
Het |
Dpf1 |
G |
T |
7: 29,010,756 (GRCm39) |
C123F |
possibly damaging |
Het |
Flvcr1 |
C |
A |
1: 190,758,206 (GRCm39) |
A29S |
probably benign |
Het |
Frmd3 |
A |
T |
4: 74,106,033 (GRCm39) |
I560F |
probably damaging |
Het |
Galnt15 |
G |
A |
14: 31,771,800 (GRCm39) |
V282I |
possibly damaging |
Het |
Gm14412 |
A |
T |
2: 177,006,405 (GRCm39) |
C497S |
probably damaging |
Het |
Gm20830 |
A |
T |
Y: 6,916,464 (GRCm39) |
Y218* |
probably null |
Het |
Hmcn2 |
C |
A |
2: 31,310,375 (GRCm39) |
T3323N |
probably damaging |
Het |
Idh1 |
T |
A |
1: 65,214,495 (GRCm39) |
Q6L |
probably benign |
Het |
Kansl2-ps |
A |
G |
7: 72,322,813 (GRCm39) |
|
noncoding transcript |
Het |
Kcnj10 |
T |
A |
1: 172,197,047 (GRCm39) |
V187E |
probably damaging |
Het |
Khnyn |
A |
G |
14: 56,124,957 (GRCm39) |
T404A |
probably damaging |
Het |
Lrp1b |
T |
A |
2: 41,660,880 (GRCm39) |
N76I |
probably damaging |
Het |
Lrrc9 |
G |
A |
12: 72,500,862 (GRCm39) |
C196Y |
probably damaging |
Het |
Ltbr |
G |
A |
6: 125,289,757 (GRCm39) |
R146W |
probably damaging |
Het |
Mgp |
T |
A |
6: 136,849,772 (GRCm39) |
N62I |
probably benign |
Het |
Ms4a6c |
T |
A |
19: 11,448,588 (GRCm39) |
H40Q |
probably benign |
Het |
Necab3 |
A |
G |
2: 154,389,379 (GRCm39) |
S121P |
probably damaging |
Het |
Nfkb1 |
T |
A |
3: 135,332,372 (GRCm39) |
K128* |
probably null |
Het |
Nr4a3 |
A |
T |
4: 48,067,861 (GRCm39) |
R486W |
probably damaging |
Het |
Nwd2 |
A |
G |
5: 63,964,991 (GRCm39) |
K1525R |
probably benign |
Het |
Odad2 |
T |
C |
18: 7,222,550 (GRCm39) |
K573R |
probably benign |
Het |
Pbrm1 |
G |
T |
14: 30,806,968 (GRCm39) |
D1085Y |
probably damaging |
Het |
R3hdm4 |
C |
T |
10: 79,748,292 (GRCm39) |
E162K |
possibly damaging |
Het |
Rbm15 |
A |
G |
3: 107,237,783 (GRCm39) |
S872P |
possibly damaging |
Het |
Retsat |
A |
G |
6: 72,578,518 (GRCm39) |
I77V |
probably damaging |
Het |
Rpl32 |
A |
G |
6: 115,783,996 (GRCm39) |
F77L |
probably benign |
Het |
Ryr3 |
A |
T |
2: 112,624,814 (GRCm39) |
V2202D |
probably damaging |
Het |
Sars2 |
G |
A |
7: 28,449,716 (GRCm39) |
R387Q |
probably null |
Het |
Serpinb3d |
G |
T |
1: 107,006,263 (GRCm39) |
T275N |
probably benign |
Het |
Sf3a1 |
C |
A |
11: 4,124,041 (GRCm39) |
P296Q |
probably damaging |
Het |
Sh3bgr |
A |
G |
16: 96,025,744 (GRCm39) |
|
probably benign |
Het |
St3gal3 |
A |
G |
4: 117,797,247 (GRCm39) |
L332P |
probably damaging |
Het |
Ston1 |
A |
G |
17: 88,952,739 (GRCm39) |
|
probably benign |
Het |
Syne2 |
T |
A |
12: 76,018,649 (GRCm39) |
S3383T |
probably damaging |
Het |
Tektl1 |
A |
T |
10: 78,584,484 (GRCm39) |
L346* |
probably null |
Het |
Tnfsf14 |
A |
G |
17: 57,499,592 (GRCm39) |
S87P |
probably benign |
Het |
Trap1 |
T |
C |
16: 3,862,529 (GRCm39) |
D583G |
probably benign |
Het |
Ube3d |
A |
T |
9: 86,309,460 (GRCm39) |
I212N |
possibly damaging |
Het |
Usp34 |
T |
A |
11: 23,362,271 (GRCm39) |
D1572E |
probably damaging |
Het |
Vmn1r179 |
A |
T |
7: 23,628,387 (GRCm39) |
T193S |
probably benign |
Het |
Vmn2r111 |
C |
A |
17: 22,767,470 (GRCm39) |
V676L |
probably damaging |
Het |
Wee1 |
TCCCC |
TCCC |
7: 109,723,776 (GRCm39) |
|
probably null |
Het |
Wls |
C |
T |
3: 159,639,976 (GRCm39) |
R536C |
probably damaging |
Het |
Zfhx3 |
A |
G |
8: 109,519,031 (GRCm39) |
D51G |
probably damaging |
Het |
|
Other mutations in Col9a2 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01331:Col9a2
|
APN |
4 |
120,902,389 (GRCm39) |
missense |
possibly damaging |
0.95 |
IGL01978:Col9a2
|
APN |
4 |
120,901,863 (GRCm39) |
missense |
unknown |
|
IGL01995:Col9a2
|
APN |
4 |
120,907,607 (GRCm39) |
critical splice donor site |
probably null |
|
IGL02162:Col9a2
|
APN |
4 |
120,911,531 (GRCm39) |
unclassified |
probably benign |
|
IGL02931:Col9a2
|
APN |
4 |
120,910,389 (GRCm39) |
missense |
probably benign |
0.06 |
collision
|
UTSW |
4 |
120,906,913 (GRCm39) |
critical splice donor site |
probably null |
|
gravity_wave
|
UTSW |
4 |
120,901,216 (GRCm39) |
critical splice donor site |
probably null |
|
R0208:Col9a2
|
UTSW |
4 |
120,909,485 (GRCm39) |
splice site |
probably benign |
|
R0426:Col9a2
|
UTSW |
4 |
120,901,857 (GRCm39) |
splice site |
probably benign |
|
R0512:Col9a2
|
UTSW |
4 |
120,911,504 (GRCm39) |
missense |
probably benign |
0.22 |
R0973:Col9a2
|
UTSW |
4 |
120,896,985 (GRCm39) |
critical splice donor site |
probably null |
|
R1023:Col9a2
|
UTSW |
4 |
120,901,207 (GRCm39) |
missense |
unknown |
|
R1657:Col9a2
|
UTSW |
4 |
120,898,171 (GRCm39) |
missense |
unknown |
|
R1724:Col9a2
|
UTSW |
4 |
120,911,099 (GRCm39) |
missense |
probably damaging |
1.00 |
R2171:Col9a2
|
UTSW |
4 |
120,902,198 (GRCm39) |
nonsense |
probably null |
|
R2206:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R2221:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R2223:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R2273:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R2274:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R2275:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R2354:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R2392:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R2393:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R2394:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R3421:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R3426:Col9a2
|
UTSW |
4 |
120,907,604 (GRCm39) |
missense |
possibly damaging |
0.93 |
R3710:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R3821:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R3838:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R3839:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R4067:Col9a2
|
UTSW |
4 |
120,909,586 (GRCm39) |
missense |
probably damaging |
1.00 |
R4298:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R4299:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R4595:Col9a2
|
UTSW |
4 |
120,902,352 (GRCm39) |
missense |
probably benign |
0.04 |
R4942:Col9a2
|
UTSW |
4 |
120,910,316 (GRCm39) |
missense |
possibly damaging |
0.73 |
R5120:Col9a2
|
UTSW |
4 |
120,896,969 (GRCm39) |
missense |
unknown |
|
R6143:Col9a2
|
UTSW |
4 |
120,911,060 (GRCm39) |
missense |
probably damaging |
0.99 |
R7027:Col9a2
|
UTSW |
4 |
120,901,216 (GRCm39) |
critical splice donor site |
probably null |
|
R7056:Col9a2
|
UTSW |
4 |
120,906,913 (GRCm39) |
critical splice donor site |
probably null |
|
R7417:Col9a2
|
UTSW |
4 |
120,911,489 (GRCm39) |
missense |
not run |
|
R7571:Col9a2
|
UTSW |
4 |
120,896,981 (GRCm39) |
missense |
unknown |
|
R9120:Col9a2
|
UTSW |
4 |
120,900,951 (GRCm39) |
splice site |
probably benign |
|
R9341:Col9a2
|
UTSW |
4 |
120,911,483 (GRCm39) |
missense |
probably benign |
0.03 |
R9343:Col9a2
|
UTSW |
4 |
120,911,483 (GRCm39) |
missense |
probably benign |
0.03 |
R9389:Col9a2
|
UTSW |
4 |
120,911,948 (GRCm39) |
missense |
probably benign |
0.00 |
R9527:Col9a2
|
UTSW |
4 |
120,899,528 (GRCm39) |
critical splice donor site |
probably null |
|
R9620:Col9a2
|
UTSW |
4 |
120,910,403 (GRCm39) |
critical splice donor site |
probably null |
|
R9784:Col9a2
|
UTSW |
4 |
120,898,226 (GRCm39) |
missense |
unknown |
|
Z1176:Col9a2
|
UTSW |
4 |
120,910,994 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- ACAGTGCAAAGACCGTGTGAC -3'
(R):5'- GCGCTAAACTTCCAGGCATC -3'
Sequencing Primer
(F):5'- CAACCTAGGGTGTAATCACGGTTTC -3'
(R):5'- AGGCATCCCCACCCCTG -3'
|
Posted On |
2017-08-14 |