Incidental Mutation 'R5573:Col9a3'
ID |
435767 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col9a3
|
Ensembl Gene |
ENSMUSG00000027570 |
Gene Name |
collagen, type IX, alpha 3 |
Synonyms |
|
MMRRC Submission |
043128-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.186)
|
Stock # |
R5573 (G1)
|
Quality Score |
214 |
Status
|
Not validated
|
Chromosome |
2 |
Chromosomal Location |
180239895-180263985 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 180261525 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Alanine to Valine
at position 605
(A605V)
|
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 benign
Transcript: ENSMUST00000103059
AA Change: A605V
PolyPhen 2
Score 0.171 (Sensitivity: 0.92; Specificity: 0.87)
|
SMART Domains |
Protein: ENSMUSP00000099348 Gene: ENSMUSG00000027570 AA Change: A605V
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 benign
Transcript: ENSMUST00000132527
AA Change: A605V
PolyPhen 2
Score 0.171 (Sensitivity: 0.92; Specificity: 0.87)
|
SMART Domains |
Protein: ENSMUSP00000128718 Gene: ENSMUSG00000027570 AA Change: A605V
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
|
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.3%
- 20x: 94.9%
|
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: 41 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Arhgef28 |
A |
T |
13: 98,065,999 (GRCm39) |
V1618D |
probably benign |
Het |
Asic5 |
T |
A |
3: 81,911,791 (GRCm39) |
F129Y |
probably benign |
Het |
Cachd1 |
A |
C |
4: 100,831,276 (GRCm39) |
K689N |
probably damaging |
Het |
Cbfa2t2 |
A |
G |
2: 154,278,782 (GRCm39) |
|
probably benign |
Het |
Cdh26 |
T |
C |
2: 178,108,482 (GRCm39) |
V360A |
probably damaging |
Het |
Csn3 |
A |
G |
5: 88,077,910 (GRCm39) |
T139A |
probably benign |
Het |
Ddx27 |
G |
T |
2: 166,859,806 (GRCm39) |
K79N |
possibly damaging |
Het |
Dhx29 |
G |
A |
13: 113,069,749 (GRCm39) |
D211N |
probably benign |
Het |
Dlg2 |
A |
G |
7: 91,646,532 (GRCm39) |
|
probably null |
Het |
Dse |
C |
A |
10: 34,028,678 (GRCm39) |
R804L |
probably benign |
Het |
Fgb |
T |
C |
3: 82,956,984 (GRCm39) |
|
probably null |
Het |
Gm11011 |
A |
T |
2: 169,429,392 (GRCm39) |
I31K |
unknown |
Het |
Hira |
A |
G |
16: 18,735,349 (GRCm39) |
T272A |
probably damaging |
Het |
Lcmt1 |
T |
A |
7: 123,000,686 (GRCm39) |
H117Q |
probably benign |
Het |
Mettl23 |
A |
G |
11: 116,734,437 (GRCm39) |
|
probably benign |
Het |
Mtmr2 |
T |
C |
9: 13,704,463 (GRCm39) |
Y197H |
probably benign |
Het |
Myo9a |
T |
G |
9: 59,778,284 (GRCm39) |
S1347A |
probably benign |
Het |
Myrfl |
A |
G |
10: 116,658,661 (GRCm39) |
V432A |
probably damaging |
Het |
Npdc1 |
G |
A |
2: 25,298,957 (GRCm39) |
D284N |
probably damaging |
Het |
Obscn |
G |
T |
11: 58,925,531 (GRCm39) |
H6347Q |
possibly damaging |
Het |
Or52r1b |
A |
T |
7: 102,691,547 (GRCm39) |
Y282F |
probably damaging |
Het |
Or8b53 |
T |
A |
9: 38,667,000 (GRCm39) |
N5K |
probably damaging |
Het |
Peg10 |
A |
G |
6: 4,755,913 (GRCm39) |
|
probably benign |
Het |
Pfkfb3 |
A |
G |
2: 11,506,483 (GRCm39) |
V10A |
probably benign |
Het |
Phf12 |
A |
G |
11: 77,915,871 (GRCm39) |
D175G |
probably damaging |
Het |
Plekhg6 |
T |
G |
6: 125,352,755 (GRCm39) |
I131L |
possibly damaging |
Het |
Ptbp3 |
A |
G |
4: 59,485,626 (GRCm39) |
V95A |
probably damaging |
Het |
Rbbp8 |
A |
G |
18: 11,855,664 (GRCm39) |
T604A |
probably benign |
Het |
Rbbp8nl |
G |
A |
2: 179,921,586 (GRCm39) |
P266L |
possibly damaging |
Het |
Ryr1 |
T |
C |
7: 28,715,148 (GRCm39) |
S4659G |
unknown |
Het |
Serpinb9d |
A |
G |
13: 33,380,423 (GRCm39) |
|
probably null |
Het |
Slc22a28 |
A |
C |
19: 8,048,462 (GRCm39) |
I395S |
possibly damaging |
Het |
Slco6c1 |
T |
A |
1: 97,055,656 (GRCm39) |
I82L |
probably benign |
Het |
Sptan1 |
C |
T |
2: 29,876,504 (GRCm39) |
R295* |
probably null |
Het |
Tdrd9 |
C |
T |
12: 111,964,336 (GRCm39) |
|
probably null |
Het |
Ube2v2 |
A |
G |
16: 15,374,343 (GRCm39) |
L77P |
possibly damaging |
Het |
Ugt3a1 |
T |
C |
15: 9,361,769 (GRCm39) |
S182P |
probably damaging |
Het |
Vwa5b1 |
T |
C |
4: 138,336,201 (GRCm39) |
E131G |
probably damaging |
Het |
Wdr18 |
C |
T |
10: 79,800,872 (GRCm39) |
A145V |
probably benign |
Het |
Xpnpep1 |
A |
G |
19: 52,993,253 (GRCm39) |
I358T |
probably damaging |
Het |
Zfp946 |
T |
A |
17: 22,673,676 (GRCm39) |
C143* |
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 |
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'- GTCAGACTTCCACAAAGCTGC -3'
(R):5'- GAACAGGCGGTATATTTAGTAGGATAC -3'
Sequencing Primer
(F):5'- TGCACTTTGGTGAACAGCC -3'
(R):5'- ACCTACTTAGCTAAAGTTAGGTACAG -3'
|
Posted On |
2016-10-24 |