Incidental Mutation 'R0890:Col9a3'
| ID |
83453 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a3
|
| Ensembl Gene |
ENSMUSG00000027570 |
| Gene Name |
collagen, type IX, alpha 3 |
| Synonyms |
|
| MMRRC Submission |
039053-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.211)
|
| Stock # |
R0890 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
2 |
| Chromosomal Location |
180239895-180263985 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 180251856 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Proline to Leucine
at position 335
(P335L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000128718
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000103059]
[ENSMUST00000132527]
|
| AlphaFold |
A2ACT7 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000103059
AA Change: P335L
PolyPhen 2
Score 0.231 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000099348
Gene: ENSMUSG00000027570
AA Change: P335L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Collagen
|
21 |
80 |
7.7e-12 |
PFAM |
|
Pfam:Collagen
|
58 |
114 |
4.2e-9 |
PFAM |
|
low complexity region
|
126 |
162 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
174 |
236 |
4.1e-12 |
PFAM |
|
Pfam:Collagen
|
213 |
292 |
8e-9 |
PFAM |
|
internal_repeat_1
|
315 |
366 |
1.58e-12 |
PROSPERO |
|
internal_repeat_2
|
360 |
382 |
2.94e-6 |
PROSPERO |
|
low complexity region
|
384 |
396 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
456 |
518 |
1.8e-11 |
PFAM |
|
Pfam:Collagen
|
545 |
606 |
3.8e-11 |
PFAM |
|
low complexity region
|
635 |
656 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129090
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000132527
AA Change: P335L
PolyPhen 2
Score 0.231 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000128718
Gene: ENSMUSG00000027570
AA Change: P335L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Collagen
|
21 |
80 |
7.9e-12 |
PFAM |
|
Pfam:Collagen
|
58 |
114 |
4.3e-9 |
PFAM |
|
Pfam:Collagen
|
109 |
166 |
4.5e-8 |
PFAM |
|
Pfam:Collagen
|
174 |
236 |
4.2e-12 |
PFAM |
|
Pfam:Collagen
|
213 |
292 |
8.2e-9 |
PFAM |
|
internal_repeat_1
|
315 |
366 |
1.58e-12 |
PROSPERO |
|
internal_repeat_2
|
360 |
382 |
2.94e-6 |
PROSPERO |
|
low complexity region
|
384 |
396 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
402 |
474 |
8.2e-8 |
PFAM |
|
Pfam:Collagen
|
456 |
518 |
1.8e-11 |
PFAM |
|
Pfam:Collagen
|
545 |
606 |
3.9e-11 |
PFAM |
|
Pfam:Collagen
|
603 |
662 |
2.5e-8 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141056
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000165879
|
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.7%
- 10x: 97.1%
- 20x: 94.0%
|
| Validation Efficiency |
|
| 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. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 32 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca15 |
T |
C |
7: 119,972,936 (GRCm39) |
S837P |
probably benign |
Het |
| Cdh24 |
A |
G |
14: 54,870,051 (GRCm39) |
V240A |
probably benign |
Het |
| Clcn4 |
T |
C |
7: 7,291,964 (GRCm39) |
T556A |
possibly damaging |
Het |
| Coa7 |
G |
A |
4: 108,195,583 (GRCm39) |
A171T |
probably damaging |
Het |
| Col12a1 |
A |
T |
9: 79,607,684 (GRCm39) |
S381R |
probably damaging |
Het |
| Dcxr |
T |
A |
11: 120,617,297 (GRCm39) |
N82I |
probably damaging |
Het |
| Dhdh |
T |
C |
7: 45,131,395 (GRCm39) |
D146G |
possibly damaging |
Het |
| Dhrs13 |
T |
A |
11: 77,925,176 (GRCm39) |
L99Q |
probably null |
Het |
| Dnai1 |
C |
T |
4: 41,604,253 (GRCm39) |
T220M |
possibly damaging |
Het |
| Gapvd1 |
T |
A |
2: 34,602,329 (GRCm39) |
D606V |
probably damaging |
Het |
| Gcn1 |
T |
G |
5: 115,717,852 (GRCm39) |
C246G |
possibly damaging |
Het |
| Gdf10 |
A |
G |
14: 33,654,113 (GRCm39) |
K207E |
possibly damaging |
Het |
| Gucy2d |
T |
C |
7: 98,122,472 (GRCm39) |
V1046A |
probably benign |
Het |
| Itpr3 |
C |
A |
17: 27,307,985 (GRCm39) |
Y257* |
probably null |
Het |
| Kifc5b |
C |
T |
17: 27,141,996 (GRCm39) |
T158M |
possibly damaging |
Het |
| Klra7 |
C |
T |
6: 130,195,916 (GRCm39) |
D251N |
probably benign |
Het |
| Mesp1 |
T |
C |
7: 79,442,683 (GRCm39) |
D198G |
probably benign |
Het |
| Mrgprb8 |
T |
A |
7: 48,038,777 (GRCm39) |
C149* |
probably null |
Het |
| Nphp4 |
C |
A |
4: 152,582,677 (GRCm39) |
L169I |
possibly damaging |
Het |
| Or1j1 |
T |
A |
2: 36,702,586 (GRCm39) |
T173S |
probably benign |
Het |
| Or52p2 |
C |
A |
7: 102,237,408 (GRCm39) |
E181* |
probably null |
Het |
| Or5h17 |
T |
A |
16: 58,820,150 (GRCm39) |
I34K |
possibly damaging |
Het |
| Pcgf5 |
A |
T |
19: 36,389,544 (GRCm39) |
H7L |
probably benign |
Het |
| Polr3b |
A |
C |
10: 84,550,200 (GRCm39) |
K970T |
probably benign |
Het |
| Pomgnt1 |
A |
G |
4: 116,009,382 (GRCm39) |
D93G |
probably benign |
Het |
| Rnf213 |
A |
G |
11: 119,321,312 (GRCm39) |
K1256E |
possibly damaging |
Het |
| Scn9a |
T |
C |
2: 66,314,079 (GRCm39) |
T1869A |
probably damaging |
Het |
| Setdb2 |
A |
G |
14: 59,656,669 (GRCm39) |
V232A |
possibly damaging |
Het |
| Sh3d21 |
T |
C |
4: 126,044,945 (GRCm39) |
E578G |
probably damaging |
Het |
| Tmem168 |
A |
T |
6: 13,603,271 (GRCm39) |
S32T |
probably damaging |
Het |
| Vmn1r38 |
T |
G |
6: 66,753,514 (GRCm39) |
I201L |
probably benign |
Het |
| Wfs1 |
C |
A |
5: 37,132,888 (GRCm39) |
W130C |
probably damaging |
Het |
|
| Other mutations in Col9a3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01022:Col9a3
|
APN |
2 |
180,258,227 (GRCm39) |
missense |
probably damaging |
0.96 |
|
IGL01542:Col9a3
|
APN |
2 |
180,251,109 (GRCm39) |
splice site |
probably benign |
|
|
IGL01727:Col9a3
|
APN |
2 |
180,258,358 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02558:Col9a3
|
APN |
2 |
180,248,599 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
IGL03112:Col9a3
|
APN |
2 |
180,249,435 (GRCm39) |
missense |
possibly damaging |
0.60 |
|
IGL02796:Col9a3
|
UTSW |
2 |
180,255,955 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0022:Col9a3
|
UTSW |
2 |
180,261,549 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0022:Col9a3
|
UTSW |
2 |
180,261,549 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0046:Col9a3
|
UTSW |
2 |
180,251,280 (GRCm39) |
missense |
possibly damaging |
0.47 |
|
R0046:Col9a3
|
UTSW |
2 |
180,251,280 (GRCm39) |
missense |
possibly damaging |
0.47 |
|
R0477:Col9a3
|
UTSW |
2 |
180,251,263 (GRCm39) |
splice site |
probably benign |
|
|
R1934:Col9a3
|
UTSW |
2 |
180,248,927 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4355:Col9a3
|
UTSW |
2 |
180,248,271 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4571:Col9a3
|
UTSW |
2 |
180,258,159 (GRCm39) |
splice site |
probably benign |
|
|
R4688:Col9a3
|
UTSW |
2 |
180,249,424 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4731:Col9a3
|
UTSW |
2 |
180,252,474 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4742:Col9a3
|
UTSW |
2 |
180,245,180 (GRCm39) |
missense |
unknown |
|
|
R4847:Col9a3
|
UTSW |
2 |
180,257,318 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4985:Col9a3
|
UTSW |
2 |
180,245,193 (GRCm39) |
missense |
unknown |
|
|
R5488:Col9a3
|
UTSW |
2 |
180,258,318 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5489:Col9a3
|
UTSW |
2 |
180,258,318 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5573:Col9a3
|
UTSW |
2 |
180,261,525 (GRCm39) |
missense |
probably benign |
0.17 |
|
R5575:Col9a3
|
UTSW |
2 |
180,240,639 (GRCm39) |
intron |
probably benign |
|
|
R6820:Col9a3
|
UTSW |
2 |
180,248,927 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7114:Col9a3
|
UTSW |
2 |
180,245,590 (GRCm39) |
missense |
unknown |
|
|
R7710:Col9a3
|
UTSW |
2 |
180,251,158 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8177:Col9a3
|
UTSW |
2 |
180,249,450 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R8342:Col9a3
|
UTSW |
2 |
180,245,183 (GRCm39) |
missense |
unknown |
|
|
R8472:Col9a3
|
UTSW |
2 |
180,247,057 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8783:Col9a3
|
UTSW |
2 |
180,255,970 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R9683:Col9a3
|
UTSW |
2 |
180,248,322 (GRCm39) |
critical splice donor site |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- CTGCATCAGGCTGAGGAGACTTTAC -3'
(R):5'- TGGATACTCACAGGGATACCTGGC -3'
Sequencing Primer
(F):5'- ATGTGGACACTATGCAGCC -3'
(R):5'- ACAGGGATACCTGGCTCTCC -3'
|
| Posted On |
2013-11-08 |
Incidental Mutation