Incidental Mutation 'R5488:Col9a3'
ID |
430446 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col9a3
|
Ensembl Gene |
ENSMUSG00000027570 |
Gene Name |
collagen, type IX, alpha 3 |
Synonyms |
|
MMRRC Submission |
043049-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.211)
|
Stock # |
R5488 (G1)
|
Quality Score |
145 |
Status
|
Validated
|
Chromosome |
2 |
Chromosomal Location |
180239895-180263985 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
G to A
at 180258318 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Arginine to Histidine
at position 579
(R579H)
|
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: R579H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000099348 Gene: ENSMUSG00000027570 AA Change: R579H
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: R579H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000128718 Gene: ENSMUSG00000027570 AA Change: R579H
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 |
0.1772 |
Coding Region Coverage |
- 1x: 98.2%
- 3x: 97.2%
- 10x: 95.1%
- 20x: 90.5%
|
Validation Efficiency |
97% (58/60) |
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: 52 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca14 |
T |
A |
7: 119,851,473 (GRCm39) |
V817D |
probably damaging |
Het |
Abca5 |
A |
G |
11: 110,183,009 (GRCm39) |
V1016A |
probably benign |
Het |
Ano2 |
G |
T |
6: 126,016,216 (GRCm39) |
M916I |
possibly damaging |
Het |
Aqr |
T |
C |
2: 113,963,554 (GRCm39) |
N632S |
probably damaging |
Het |
Cd48 |
G |
A |
1: 171,523,273 (GRCm39) |
V39I |
possibly damaging |
Het |
Cdcp3 |
A |
G |
7: 130,848,324 (GRCm39) |
D710G |
probably damaging |
Het |
Cdk17 |
A |
G |
10: 93,068,274 (GRCm39) |
T344A |
probably damaging |
Het |
Chd8 |
A |
T |
14: 52,450,505 (GRCm39) |
|
probably benign |
Het |
Col4a1 |
A |
T |
8: 11,362,550 (GRCm39) |
|
probably benign |
Het |
Cripto |
G |
A |
9: 110,772,265 (GRCm39) |
R44C |
probably benign |
Het |
Cyp2c69 |
T |
G |
19: 39,839,603 (GRCm39) |
Q340P |
probably null |
Het |
D630003M21Rik |
T |
A |
2: 158,058,941 (GRCm39) |
T320S |
probably benign |
Het |
D630045J12Rik |
A |
T |
6: 38,173,782 (GRCm39) |
S129T |
possibly damaging |
Het |
Eif4a3l1 |
C |
G |
6: 136,306,555 (GRCm39) |
R339G |
probably damaging |
Het |
Fam13a |
A |
T |
6: 59,001,303 (GRCm39) |
L8Q |
probably null |
Het |
Fam83b |
T |
C |
9: 76,452,881 (GRCm39) |
N62S |
probably benign |
Het |
Foxred1 |
A |
T |
9: 35,121,266 (GRCm39) |
V94E |
probably damaging |
Het |
Gprc5a |
T |
C |
6: 135,055,868 (GRCm39) |
V105A |
probably damaging |
Het |
Gvin3 |
T |
A |
7: 106,200,797 (GRCm39) |
|
noncoding transcript |
Het |
Itga2 |
A |
T |
13: 114,979,971 (GRCm39) |
W1077R |
probably damaging |
Het |
Kat6b |
A |
G |
14: 21,719,332 (GRCm39) |
D1228G |
probably damaging |
Het |
Kctd3 |
A |
G |
1: 188,713,563 (GRCm39) |
Y391H |
probably damaging |
Het |
Kdelr2 |
T |
A |
5: 143,389,784 (GRCm39) |
I23N |
probably damaging |
Het |
Kmt2a |
A |
T |
9: 44,752,335 (GRCm39) |
|
probably benign |
Het |
Lao1 |
A |
G |
4: 118,824,566 (GRCm39) |
E216G |
probably damaging |
Het |
Mark4 |
G |
T |
7: 19,163,532 (GRCm39) |
|
probably null |
Het |
Mcm10 |
A |
G |
2: 4,996,929 (GRCm39) |
W851R |
probably damaging |
Het |
Mettl21e |
T |
C |
1: 44,257,276 (GRCm39) |
Y14C |
probably benign |
Het |
Miga1 |
CACAACAACAACAACAACA |
CACAACAACAACAACA |
3: 152,039,083 (GRCm39) |
|
probably benign |
Het |
Mmp20 |
A |
G |
9: 7,643,958 (GRCm39) |
|
probably null |
Het |
Nlrp5 |
A |
T |
7: 23,117,359 (GRCm39) |
D361V |
probably benign |
Het |
Nrip3 |
T |
C |
7: 109,361,045 (GRCm39) |
T210A |
probably damaging |
Het |
Or12d2 |
T |
C |
17: 37,624,559 (GRCm39) |
T239A |
probably damaging |
Het |
Or52s1b |
T |
C |
7: 102,822,658 (GRCm39) |
Y62C |
probably damaging |
Het |
Pcdh10 |
G |
A |
3: 45,335,803 (GRCm39) |
G706S |
probably damaging |
Het |
Pdzd2 |
G |
A |
15: 12,382,762 (GRCm39) |
P1197L |
probably benign |
Het |
Pfkfb3 |
T |
C |
2: 11,489,480 (GRCm39) |
S273G |
probably benign |
Het |
Pkn3 |
T |
C |
2: 29,978,596 (GRCm39) |
|
probably null |
Het |
Rab40c |
G |
A |
17: 26,109,643 (GRCm39) |
T78I |
probably damaging |
Het |
Rec8 |
A |
T |
14: 55,860,283 (GRCm39) |
Q291L |
probably benign |
Het |
Robo4 |
CGG |
CG |
9: 37,322,786 (GRCm39) |
|
probably null |
Het |
Sart3 |
A |
G |
5: 113,909,441 (GRCm39) |
W86R |
probably damaging |
Het |
Slc6a11 |
A |
G |
6: 114,220,855 (GRCm39) |
D462G |
probably damaging |
Het |
Syne2 |
A |
G |
12: 75,934,946 (GRCm39) |
T143A |
probably benign |
Het |
Tardbp |
A |
G |
4: 148,703,097 (GRCm39) |
F289S |
probably benign |
Het |
Tdpoz1 |
T |
A |
3: 93,577,974 (GRCm39) |
Y270F |
possibly damaging |
Het |
Tmem117 |
ACCC |
ACC |
15: 94,992,698 (GRCm39) |
|
probably null |
Het |
Trim43a |
A |
T |
9: 88,464,229 (GRCm39) |
I47F |
probably damaging |
Het |
Vim |
A |
T |
2: 13,580,392 (GRCm39) |
T202S |
probably benign |
Het |
Vps13b |
A |
T |
15: 35,770,688 (GRCm39) |
I2044L |
probably benign |
Het |
Wdr5 |
T |
G |
2: 27,415,165 (GRCm39) |
D192E |
probably damaging |
Het |
Zmym2 |
A |
G |
14: 57,193,712 (GRCm39) |
K1176E |
possibly 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 |
|
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 |
|
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'- TGGTAATCCTCTCTGAAGTATGCAC -3'
(R):5'- CCTGAGTGTTCCTTGAGTCC -3'
Sequencing Primer
(F):5'- CTGAAGTATGCACTTGACACTCTG -3'
(R):5'- GAGTCCTCTCTTCCCTGGAC -3'
|
Posted On |
2016-10-05 |