Incidental Mutation 'R6820:Col9a3'
| ID |
537555 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a3
|
| Ensembl Gene |
ENSMUSG00000027570 |
| Gene Name |
collagen, type IX, alpha 3 |
| Synonyms |
|
| MMRRC Submission |
044932-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.211)
|
| Stock # |
R6820 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
180239895-180263985 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 180248927 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Methionine
at position 260
(V260M)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000128718
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000103059]
[ENSMUST00000132527]
|
| AlphaFold |
A2ACT7 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000103059
AA Change: V260M
PolyPhen 2
Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000099348
Gene: ENSMUSG00000027570
AA Change: V260M
| 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 damaging
Transcript: ENSMUST00000132527
AA Change: V260M
PolyPhen 2
Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000128718
Gene: ENSMUSG00000027570
AA Change: V260M
| 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
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.7%
|
| Validation Efficiency |
98% (46/47) |
| 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: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Accs |
T |
A |
2: 93,673,266 (GRCm39) |
N141Y |
probably null |
Het |
| Chkb |
A |
G |
15: 89,312,379 (GRCm39) |
L46P |
probably damaging |
Het |
| Dna2 |
T |
C |
10: 62,800,683 (GRCm39) |
I739T |
possibly damaging |
Het |
| Dnah17 |
T |
C |
11: 117,959,826 (GRCm39) |
H2620R |
probably damaging |
Het |
| Dsel |
A |
G |
1: 111,787,547 (GRCm39) |
V996A |
probably damaging |
Het |
| Dst |
T |
C |
1: 34,250,337 (GRCm39) |
L1757S |
probably damaging |
Het |
| Exoc5 |
A |
T |
14: 49,286,387 (GRCm39) |
|
probably null |
Het |
| Fam120a |
A |
T |
13: 49,034,468 (GRCm39) |
V1048E |
possibly damaging |
Het |
| Fam50b |
G |
A |
13: 34,931,084 (GRCm39) |
E187K |
possibly damaging |
Het |
| Fbxw19 |
T |
A |
9: 109,311,079 (GRCm39) |
T377S |
probably benign |
Het |
| Fbxw28 |
A |
T |
9: 109,167,493 (GRCm39) |
F88Y |
probably damaging |
Het |
| Grik5 |
C |
T |
7: 24,745,780 (GRCm39) |
R431Q |
possibly damaging |
Het |
| Gtsf1 |
T |
C |
15: 103,328,954 (GRCm39) |
T92A |
probably benign |
Het |
| Hoxc13 |
A |
G |
15: 102,830,257 (GRCm39) |
Y212C |
probably damaging |
Het |
| Itih2 |
T |
C |
2: 10,102,909 (GRCm39) |
I742V |
probably benign |
Het |
| Kat7 |
T |
C |
11: 95,174,965 (GRCm39) |
T351A |
probably damaging |
Het |
| Mlh3 |
T |
C |
12: 85,294,497 (GRCm39) |
D1233G |
probably damaging |
Het |
| Mroh2b |
A |
G |
15: 4,982,756 (GRCm39) |
D1525G |
probably damaging |
Het |
| Nme5 |
T |
C |
18: 34,704,626 (GRCm39) |
Y73C |
probably damaging |
Het |
| Nr3c2 |
T |
C |
8: 77,969,086 (GRCm39) |
V957A |
probably damaging |
Het |
| Nup153 |
A |
G |
13: 46,863,459 (GRCm39) |
S301P |
probably benign |
Het |
| Obscn |
T |
C |
11: 58,942,019 (GRCm39) |
D5013G |
probably damaging |
Het |
| Or4f54 |
C |
T |
2: 111,123,455 (GRCm39) |
P281S |
probably damaging |
Het |
| Or5p51 |
A |
G |
7: 107,444,298 (GRCm39) |
V214A |
probably benign |
Het |
| Or8g51 |
A |
G |
9: 38,608,771 (GRCm39) |
V297A |
possibly damaging |
Het |
| Pak1 |
A |
G |
7: 97,535,586 (GRCm39) |
N226D |
probably benign |
Het |
| Pak4 |
A |
G |
7: 28,262,461 (GRCm39) |
Y384H |
probably benign |
Het |
| Pkp3 |
T |
C |
7: 140,659,757 (GRCm39) |
|
probably null |
Het |
| Prxl2b |
A |
T |
4: 154,982,623 (GRCm39) |
D50E |
probably damaging |
Het |
| Psd |
G |
T |
19: 46,309,283 (GRCm39) |
A558E |
probably damaging |
Het |
| Psmd14 |
C |
A |
2: 61,607,068 (GRCm39) |
H172N |
probably benign |
Het |
| Pygb |
G |
T |
2: 150,658,674 (GRCm39) |
W366L |
possibly damaging |
Het |
| Rbm39 |
A |
T |
2: 156,021,146 (GRCm39) |
M1K |
probably null |
Het |
| Rnf213 |
T |
C |
11: 119,339,664 (GRCm39) |
I3421T |
probably damaging |
Het |
| Rsf1 |
ATGGCG |
ATGGCGACGGTGGCG |
7: 97,229,111 (GRCm39) |
|
probably benign |
Het |
| Smg6 |
T |
C |
11: 74,932,790 (GRCm39) |
V88A |
probably damaging |
Het |
| Tha1 |
T |
C |
11: 117,762,504 (GRCm39) |
E80G |
probably benign |
Het |
| Tie1 |
A |
G |
4: 118,341,583 (GRCm39) |
V243A |
probably damaging |
Het |
| Tmem215 |
T |
C |
4: 40,473,926 (GRCm39) |
M1T |
probably null |
Het |
| Tpm2 |
A |
G |
4: 43,518,443 (GRCm39) |
Y221H |
probably damaging |
Het |
| Ubap1 |
C |
T |
4: 41,379,854 (GRCm39) |
P356L |
probably benign |
Het |
| Wbp2nl |
G |
T |
15: 82,197,996 (GRCm39) |
A178S |
possibly damaging |
Het |
| Wdr54 |
A |
T |
6: 83,131,601 (GRCm39) |
S139T |
probably benign |
Het |
| Wipi2 |
G |
C |
5: 142,615,555 (GRCm39) |
Q14H |
probably benign |
Het |
| Zan |
T |
C |
5: 137,406,106 (GRCm39) |
|
probably benign |
Het |
| Zfp735 |
A |
G |
11: 73,579,783 (GRCm39) |
M1V |
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 |
|
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 |
|
|
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'- GTCTCACCAGTCAGCATCAC -3'
(R):5'- ATCGGCATGCCACATTGTCC -3'
Sequencing Primer
(F):5'- ACCAAAGCTCTTCCTGGCTGG -3'
(R):5'- GTGCCCTGGACCTCATGGATATAC -3'
|
| Posted On |
2018-10-18 |
Incidental Mutation