Incidental Mutation 'R0022:Col9a3'
| ID |
15235 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a3
|
| Ensembl Gene |
ENSMUSG00000027570 |
| Gene Name |
collagen, type IX, alpha 3 |
| Synonyms |
|
| MMRRC Submission |
038317-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.186)
|
| Stock # |
R0022 (G1)
|
| Quality Score |
|
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
180239895-180263985 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 180261549 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 613
(D613G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000128718
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037877]
[ENSMUST00000103059]
[ENSMUST00000132527]
|
| AlphaFold |
A2ACT7 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000037877
|
| SMART Domains |
Protein: ENSMUSP00000040611
Gene: ENSMUSG00000038932
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
36 |
N/A |
INTRINSIC |
|
low complexity region
|
76 |
110 |
N/A |
INTRINSIC |
|
low complexity region
|
152 |
167 |
N/A |
INTRINSIC |
|
low complexity region
|
185 |
198 |
N/A |
INTRINSIC |
|
low complexity region
|
355 |
373 |
N/A |
INTRINSIC |
|
HLH
|
395 |
445 |
2.13e-9 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000103059
AA Change: D613G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000099348
Gene: ENSMUSG00000027570
AA Change: D613G
| 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 |
probably damaging
Transcript: ENSMUST00000132527
AA Change: D613G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000128718
Gene: ENSMUSG00000027570
AA Change: D613G
| 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: ENSMUST00000165224
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000165879
|
| Meta Mutation Damage Score |
0.1186 |
| Coding Region Coverage |
- 1x: 82.0%
- 3x: 74.9%
- 10x: 56.1%
- 20x: 37.0%
|
| Validation Efficiency |
97% (90/93) |
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aste1 |
T |
A |
9: 105,273,823 (GRCm39) |
L21* |
probably null |
Het |
| Btbd10 |
G |
A |
7: 112,924,988 (GRCm39) |
Q287* |
probably null |
Het |
| Cd244a |
A |
G |
1: 171,401,330 (GRCm39) |
D48G |
probably benign |
Het |
| Cdc20 |
T |
A |
4: 118,292,686 (GRCm39) |
H354L |
probably damaging |
Het |
| Cdhr3 |
G |
A |
12: 33,132,263 (GRCm39) |
T120I |
probably damaging |
Het |
| Chd8 |
A |
T |
14: 52,470,312 (GRCm39) |
S433T |
probably benign |
Het |
| Col1a2 |
G |
A |
6: 4,518,822 (GRCm39) |
|
probably benign |
Het |
| Coro7 |
C |
T |
16: 4,451,168 (GRCm39) |
R507H |
probably benign |
Het |
| Cracdl |
C |
T |
1: 37,667,326 (GRCm39) |
R240Q |
probably damaging |
Het |
| Csf1 |
A |
T |
3: 107,661,178 (GRCm39) |
V113E |
probably damaging |
Het |
| Dclre1b |
G |
T |
3: 103,710,464 (GRCm39) |
H482Q |
probably benign |
Het |
| Ephb6 |
T |
C |
6: 41,591,503 (GRCm39) |
V220A |
probably damaging |
Het |
| Ggct |
C |
A |
6: 54,962,887 (GRCm39) |
E175* |
probably null |
Het |
| Gm5316 |
T |
C |
6: 122,877,354 (GRCm39) |
|
noncoding transcript |
Het |
| Gzmn |
A |
G |
14: 56,404,382 (GRCm39) |
S152P |
probably damaging |
Het |
| Hoxa7 |
T |
C |
6: 52,194,363 (GRCm39) |
N8S |
probably damaging |
Het |
| Il12rb2 |
A |
G |
6: 67,275,903 (GRCm39) |
F630S |
probably damaging |
Het |
| Kit |
A |
G |
5: 75,783,657 (GRCm39) |
N378S |
probably benign |
Het |
| Lrp1b |
A |
T |
2: 40,888,050 (GRCm39) |
|
probably benign |
Het |
| Ltbp1 |
T |
A |
17: 75,671,355 (GRCm39) |
V1194D |
probably damaging |
Het |
| Mc5r |
T |
G |
18: 68,471,853 (GRCm39) |
S71A |
probably benign |
Het |
| Mcc |
C |
G |
18: 44,652,583 (GRCm39) |
|
probably benign |
Het |
| Naa25 |
C |
A |
5: 121,556,039 (GRCm39) |
L276M |
probably damaging |
Het |
| Nlrp1b |
T |
G |
11: 71,052,755 (GRCm39) |
K888T |
possibly damaging |
Het |
| Pabpc6 |
A |
T |
17: 9,888,145 (GRCm39) |
N135K |
probably benign |
Het |
| Pik3r2 |
A |
G |
8: 71,223,545 (GRCm39) |
F346S |
probably damaging |
Het |
| Pkd1 |
T |
C |
17: 24,813,793 (GRCm39) |
W4086R |
probably damaging |
Het |
| Pmfbp1 |
C |
T |
8: 110,252,039 (GRCm39) |
R395W |
probably damaging |
Het |
| Ppp1ca |
T |
G |
19: 4,244,580 (GRCm39) |
V213G |
possibly damaging |
Het |
| Ptpro |
T |
A |
6: 137,420,592 (GRCm39) |
V1007D |
probably damaging |
Het |
| Rapgef2 |
G |
A |
3: 78,995,207 (GRCm39) |
R814C |
probably damaging |
Het |
| Rnasel |
A |
T |
1: 153,636,521 (GRCm39) |
I634F |
probably damaging |
Het |
| Rnf157 |
A |
T |
11: 116,240,276 (GRCm39) |
|
probably benign |
Het |
| Ryr3 |
A |
G |
2: 112,471,011 (GRCm39) |
S4567P |
probably damaging |
Het |
| Sephs1 |
A |
G |
2: 4,904,371 (GRCm39) |
T250A |
probably benign |
Het |
| Smcr8 |
T |
A |
11: 60,671,185 (GRCm39) |
W778R |
probably damaging |
Het |
| Stat1 |
T |
A |
1: 52,179,789 (GRCm39) |
L333Q |
probably damaging |
Het |
| Taar1 |
G |
T |
10: 23,796,625 (GRCm39) |
A108S |
probably benign |
Het |
| Tro |
C |
G |
X: 149,430,508 (GRCm39) |
|
probably benign |
Het |
| Ubr1 |
A |
T |
2: 120,791,654 (GRCm39) |
|
probably benign |
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 |
|
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 |
|
|
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 |
|
|
| Posted On |
2012-12-12 |
Incidental Mutation