Incidental Mutation 'R4742:Col9a3'
| ID |
358120 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a3
|
| Ensembl Gene |
ENSMUSG00000027570 |
| Gene Name |
collagen, type IX, alpha 3 |
| Synonyms |
|
| MMRRC Submission |
041966-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.186)
|
| Stock # |
R4742 (G1)
|
| Quality Score |
191 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
180239895-180263985 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 180245180 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glycine to Tryptophan
at position 130
(G130W)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000128718
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000103059]
[ENSMUST00000132527]
|
| AlphaFold |
A2ACT7 |
| Predicted Effect |
unknown
Transcript: ENSMUST00000103059
AA Change: G130W
|
| SMART Domains |
Protein: ENSMUSP00000099348
Gene: ENSMUSG00000027570
AA Change: G130W
| 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 |
unknown
Transcript: ENSMUST00000132527
AA Change: G130W
|
| SMART Domains |
Protein: ENSMUSP00000128718
Gene: ENSMUSG00000027570
AA Change: G130W
| 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
|
| Meta Mutation Damage Score |
0.2751 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 93.9%
|
| Validation Efficiency |
94% (51/54) |
| 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: 47 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 8030423J24Rik |
G |
T |
13: 71,031,644 (GRCm39) |
R17L |
unknown |
Het |
| Acan |
T |
C |
7: 78,750,517 (GRCm39) |
F1763L |
probably benign |
Het |
| Adgrb1 |
T |
A |
15: 74,401,328 (GRCm39) |
L108* |
probably null |
Het |
| Anapc2 |
T |
A |
2: 25,163,555 (GRCm39) |
|
probably null |
Het |
| Apbb1ip |
A |
G |
2: 22,716,928 (GRCm39) |
K177E |
unknown |
Het |
| Azgp1 |
T |
A |
5: 137,987,888 (GRCm39) |
Y223* |
probably null |
Het |
| Cfap44 |
T |
G |
16: 44,269,615 (GRCm39) |
|
probably null |
Het |
| Chfr |
C |
T |
5: 110,291,464 (GRCm39) |
T94I |
probably benign |
Het |
| Chrna10 |
T |
G |
7: 101,762,344 (GRCm39) |
Q282P |
probably damaging |
Het |
| Dcaf1 |
A |
G |
9: 106,735,754 (GRCm39) |
T901A |
probably benign |
Het |
| Dock2 |
T |
G |
11: 34,244,170 (GRCm39) |
|
probably null |
Het |
| Dysf |
C |
A |
6: 84,074,697 (GRCm39) |
D499E |
probably damaging |
Het |
| Fdxacb1 |
A |
G |
9: 50,679,968 (GRCm39) |
|
probably benign |
Het |
| Fhip1b |
A |
G |
7: 105,033,518 (GRCm39) |
V566A |
probably damaging |
Het |
| Il31ra |
G |
T |
13: 112,660,501 (GRCm39) |
S615* |
probably null |
Het |
| Itgam |
C |
T |
7: 127,712,245 (GRCm39) |
S827F |
probably damaging |
Het |
| Mapkbp1 |
T |
A |
2: 119,847,299 (GRCm39) |
V512E |
probably damaging |
Het |
| Myo1c |
C |
T |
11: 75,560,856 (GRCm39) |
R770* |
probably null |
Het |
| Nab2 |
T |
C |
10: 127,498,696 (GRCm39) |
T458A |
probably benign |
Het |
| Nadsyn1 |
A |
G |
7: 143,352,367 (GRCm39) |
|
probably benign |
Het |
| Nek10 |
A |
G |
14: 14,861,624 (GRCm38) |
D560G |
probably null |
Het |
| Or2ag13 |
A |
T |
7: 106,472,635 (GRCm39) |
N272K |
probably damaging |
Het |
| Or2ak6 |
A |
G |
11: 58,592,685 (GRCm39) |
R53G |
probably benign |
Het |
| Or8b46 |
T |
C |
9: 38,450,952 (GRCm39) |
S254P |
probably damaging |
Het |
| Pou1f1 |
C |
A |
16: 65,320,367 (GRCm39) |
P19T |
probably benign |
Het |
| Prdm9 |
A |
T |
17: 15,773,783 (GRCm39) |
D329E |
probably damaging |
Het |
| Prkn |
T |
A |
17: 11,456,591 (GRCm39) |
|
probably null |
Het |
| Ptprm |
A |
C |
17: 67,051,746 (GRCm39) |
Y962* |
probably null |
Het |
| Rad9a |
G |
A |
19: 4,250,560 (GRCm39) |
R85C |
probably damaging |
Het |
| Rhox2c |
A |
C |
X: 36,635,351 (GRCm39) |
Q4H |
probably benign |
Het |
| Rlig1 |
T |
C |
10: 100,414,243 (GRCm39) |
I139V |
probably benign |
Het |
| Rtkn2 |
A |
G |
10: 67,839,144 (GRCm39) |
T154A |
possibly damaging |
Het |
| Slitrk3 |
T |
C |
3: 72,955,898 (GRCm39) |
D958G |
probably benign |
Het |
| Spata31d1b |
C |
A |
13: 59,864,426 (GRCm39) |
H525N |
probably damaging |
Het |
| Tacc2 |
A |
G |
7: 130,227,697 (GRCm39) |
R1461G |
probably benign |
Het |
| Tas2r105 |
G |
A |
6: 131,663,814 (GRCm39) |
H205Y |
probably damaging |
Het |
| Tenm4 |
A |
G |
7: 96,446,691 (GRCm39) |
N809D |
probably damaging |
Het |
| Thoc2l |
A |
T |
5: 104,666,723 (GRCm39) |
N415I |
probably benign |
Het |
| Tns1 |
A |
G |
1: 74,163,449 (GRCm39) |
|
probably null |
Het |
| Top1 |
A |
G |
2: 160,545,490 (GRCm39) |
|
probably null |
Het |
| Traf3ip2 |
C |
T |
10: 39,515,256 (GRCm39) |
P345S |
possibly damaging |
Het |
| Ttn |
T |
A |
2: 76,585,168 (GRCm39) |
I22042F |
probably damaging |
Het |
| Txndc9 |
T |
C |
1: 38,026,765 (GRCm39) |
D135G |
possibly damaging |
Het |
| Usp3 |
A |
G |
9: 66,427,959 (GRCm39) |
Y339H |
probably damaging |
Het |
| Vmn1r5 |
A |
T |
6: 56,963,236 (GRCm39) |
K304* |
probably null |
Het |
| Vmn2r92 |
A |
G |
17: 18,387,119 (GRCm39) |
T153A |
probably benign |
Het |
| Xkr5 |
A |
T |
8: 18,998,746 (GRCm39) |
*55K |
probably null |
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 |
|
|
R0890:Col9a3
|
UTSW |
2 |
180,251,856 (GRCm39) |
missense |
probably benign |
0.23 |
|
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 |
|
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'- AATAGCCCAGATCGTGGTGG -3'
(R):5'- TGTCTGCCACCCTGAGTCATAG -3'
Sequencing Primer
(F):5'- GAGTGGTCTCCTTAGGGGACATC -3'
(R):5'- AGTCATAGGCGGCTCTCTGTC -3'
|
| Posted On |
2015-11-11 |
Incidental Mutation