Incidental Mutation 'R9341:Col9a2'
| ID |
707483 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a2
|
| Ensembl Gene |
ENSMUSG00000028626 |
| Gene Name |
collagen, type IX, alpha 2 |
| Synonyms |
Col9a-2 |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R9341 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
121039385-121055322 bp(+) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 121054286 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Lysine
at position 608
(M608K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000030372
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030372]
[ENSMUST00000058754]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030372
AA Change: M608K
PolyPhen 2
Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000030372
Gene: ENSMUSG00000028626
AA Change: M608K
| 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 |
probably benign
Transcript: ENSMUST00000058754
|
| SMART Domains |
Protein: ENSMUSP00000053900
Gene: ENSMUSG00000043207
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Peptidase_M48_N
|
41 |
225 |
2.5e-70 |
PFAM |
|
Pfam:Peptidase_M48
|
228 |
473 |
5.5e-75 |
PFAM |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.2%
|
| Validation Efficiency |
100% (48/48) |
| 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: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acat2 |
T |
C |
17: 12,948,651 |
N166S |
probably damaging |
Het |
| Agap2 |
G |
C |
10: 127,091,690 |
G1147R |
unknown |
Het |
| Atp8b2 |
A |
T |
3: 89,948,504 |
F446I |
possibly damaging |
Het |
| Cacna2d3 |
A |
T |
14: 28,982,358 |
M822K |
possibly damaging |
Het |
| Caskin1 |
A |
G |
17: 24,504,473 |
E745G |
probably damaging |
Het |
| Clec4a2 |
G |
T |
6: 123,127,996 |
A82S |
probably benign |
Het |
| Col5a3 |
T |
C |
9: 20,793,613 |
N749S |
unknown |
Het |
| Cope |
T |
C |
8: 70,308,578 |
|
probably null |
Het |
| Dennd2d |
T |
A |
3: 106,490,414 |
|
probably null |
Het |
| Dpys |
T |
C |
15: 39,793,352 |
T440A |
possibly damaging |
Het |
| Fam186b |
G |
A |
15: 99,279,735 |
A570V |
probably damaging |
Het |
| Fbln5 |
G |
A |
12: 101,771,292 |
T152I |
probably damaging |
Het |
| Gm16503 |
A |
T |
4: 147,541,051 |
M1L |
unknown |
Het |
| Gm9195 |
A |
G |
14: 72,480,060 |
S278P |
probably damaging |
Het |
| Hmcn2 |
A |
G |
2: 31,389,347 |
N1787S |
probably benign |
Het |
| Klhl33 |
A |
G |
14: 50,896,446 |
|
probably null |
Het |
| Lrrk2 |
A |
G |
15: 91,700,415 |
D345G |
probably benign |
Het |
| Man2b2 |
A |
G |
5: 36,818,607 |
L368P |
probably damaging |
Het |
| Med23 |
T |
A |
10: 24,912,807 |
S1371T |
probably benign |
Het |
| Mllt3 |
T |
A |
4: 87,873,931 |
E109D |
possibly damaging |
Het |
| Myom2 |
G |
A |
8: 15,084,633 |
D479N |
probably damaging |
Het |
| Olfr584 |
A |
T |
7: 103,086,117 |
R195* |
probably null |
Het |
| Pcdhga10 |
G |
T |
18: 37,747,479 |
A98S |
probably benign |
Het |
| Pde8a |
A |
T |
7: 81,300,679 |
Q221H |
probably benign |
Het |
| Pkd1l1 |
T |
C |
11: 8,836,399 |
H2335R |
|
Het |
| Pkd1l1 |
T |
A |
11: 8,961,305 |
D324V |
|
Het |
| Pou2f2 |
G |
A |
7: 25,094,852 |
T363I |
possibly damaging |
Het |
| Prlr |
A |
G |
15: 10,328,902 |
I488V |
probably benign |
Het |
| Psmd2 |
T |
C |
16: 20,656,691 |
|
probably null |
Het |
| Rbm7 |
T |
C |
9: 48,489,669 |
D253G |
probably damaging |
Het |
| Ros1 |
A |
G |
10: 52,096,020 |
|
probably null |
Het |
| S1pr3 |
G |
T |
13: 51,419,517 |
V245L |
probably damaging |
Het |
| Sacs |
A |
G |
14: 61,208,770 |
D2755G |
probably benign |
Het |
| Scgn |
T |
A |
13: 23,989,846 |
|
probably null |
Het |
| Sh3rf3 |
A |
G |
10: 59,130,980 |
K715E |
probably damaging |
Het |
| Sox18 |
T |
C |
2: 181,670,438 |
E300G |
probably damaging |
Het |
| Spef2 |
T |
A |
15: 9,713,104 |
N394I |
probably damaging |
Het |
| Strn4 |
T |
C |
7: 16,839,902 |
F759L |
probably damaging |
Het |
| Tas2r144 |
A |
T |
6: 42,216,132 |
I269F |
probably benign |
Het |
| Tpcn1 |
T |
C |
5: 120,540,672 |
D606G |
possibly damaging |
Het |
| Trh |
A |
G |
6: 92,243,842 |
I13T |
probably benign |
Het |
| Umodl1 |
T |
C |
17: 30,998,727 |
I1169T |
possibly damaging |
Het |
| Vwa3b |
G |
A |
1: 37,114,534 |
D486N |
probably damaging |
Het |
| Wars2 |
T |
C |
3: 99,187,530 |
L47P |
probably benign |
Het |
| Zbtb14 |
A |
G |
17: 69,388,581 |
S425G |
probably damaging |
Het |
| Zdhhc16 |
T |
C |
19: 41,938,110 |
S111P |
probably benign |
Het |
|
| Other mutations in Col9a2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01331:Col9a2
|
APN |
4 |
121,045,192 (GRCm38) |
missense |
possibly damaging |
0.95 |
|
IGL01978:Col9a2
|
APN |
4 |
121,044,666 (GRCm38) |
missense |
unknown |
|
|
IGL01995:Col9a2
|
APN |
4 |
121,050,410 (GRCm38) |
critical splice donor site |
probably null |
|
|
IGL02162:Col9a2
|
APN |
4 |
121,054,334 (GRCm38) |
unclassified |
probably benign |
|
|
IGL02931:Col9a2
|
APN |
4 |
121,053,192 (GRCm38) |
missense |
probably benign |
0.06 |
|
collision
|
UTSW |
4 |
121,049,716 (GRCm38) |
critical splice donor site |
probably null |
|
|
gravity_wave
|
UTSW |
4 |
121,044,019 (GRCm38) |
critical splice donor site |
probably null |
|
|
R0208:Col9a2
|
UTSW |
4 |
121,052,288 (GRCm38) |
splice site |
probably benign |
|
|
R0426:Col9a2
|
UTSW |
4 |
121,044,660 (GRCm38) |
splice site |
probably benign |
|
|
R0512:Col9a2
|
UTSW |
4 |
121,054,307 (GRCm38) |
missense |
probably benign |
0.22 |
|
R0973:Col9a2
|
UTSW |
4 |
121,039,788 (GRCm38) |
critical splice donor site |
probably null |
|
|
R1023:Col9a2
|
UTSW |
4 |
121,044,010 (GRCm38) |
missense |
unknown |
|
|
R1657:Col9a2
|
UTSW |
4 |
121,040,974 (GRCm38) |
missense |
unknown |
|
|
R1724:Col9a2
|
UTSW |
4 |
121,053,902 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R2171:Col9a2
|
UTSW |
4 |
121,045,001 (GRCm38) |
nonsense |
probably null |
|
|
R2206:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2221:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2223:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2273:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2274:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2275:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2354:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2392:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2393:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2394:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R3421:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R3426:Col9a2
|
UTSW |
4 |
121,050,407 (GRCm38) |
missense |
possibly damaging |
0.93 |
|
R3710:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R3821:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R3838:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R3839:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R4067:Col9a2
|
UTSW |
4 |
121,052,389 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4298:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R4299:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R4595:Col9a2
|
UTSW |
4 |
121,045,155 (GRCm38) |
missense |
probably benign |
0.04 |
|
R4942:Col9a2
|
UTSW |
4 |
121,053,119 (GRCm38) |
missense |
possibly damaging |
0.73 |
|
R5120:Col9a2
|
UTSW |
4 |
121,039,772 (GRCm38) |
missense |
unknown |
|
|
R5434:Col9a2
|
UTSW |
4 |
121,040,965 (GRCm38) |
nonsense |
probably null |
|
|
R6143:Col9a2
|
UTSW |
4 |
121,053,863 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R7027:Col9a2
|
UTSW |
4 |
121,044,019 (GRCm38) |
critical splice donor site |
probably null |
|
|
R7056:Col9a2
|
UTSW |
4 |
121,049,716 (GRCm38) |
critical splice donor site |
probably null |
|
|
R7417:Col9a2
|
UTSW |
4 |
121,054,292 (GRCm38) |
missense |
not run |
|
|
R7571:Col9a2
|
UTSW |
4 |
121,039,784 (GRCm38) |
missense |
unknown |
|
|
R9120:Col9a2
|
UTSW |
4 |
121,043,754 (GRCm38) |
splice site |
probably benign |
|
|
R9343:Col9a2
|
UTSW |
4 |
121,054,286 (GRCm38) |
missense |
probably benign |
0.03 |
|
R9389:Col9a2
|
UTSW |
4 |
121,054,751 (GRCm38) |
missense |
probably benign |
0.00 |
|
R9527:Col9a2
|
UTSW |
4 |
121,042,331 (GRCm38) |
critical splice donor site |
probably null |
|
|
R9620:Col9a2
|
UTSW |
4 |
121,053,206 (GRCm38) |
critical splice donor site |
probably null |
|
|
R9784:Col9a2
|
UTSW |
4 |
121,041,029 (GRCm38) |
missense |
unknown |
|
|
Z1176:Col9a2
|
UTSW |
4 |
121,053,797 (GRCm38) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TACAGAACCTCCCAAATCTTATCTGG -3'
(R):5'- TCAAGAGTCCCAACTGCCAG -3'
Sequencing Primer
(F):5'- AACCTCCCAAATCTTATCTGGATCTC -3'
(R):5'- GTCCCAACTGCCAGCTCCC -3'
|
| Posted On |
2022-04-18 |
Incidental Mutation