Incidental Mutation 'R4067:Col9a2'
| ID |
316157 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a2
|
| Ensembl Gene |
ENSMUSG00000028626 |
| Gene Name |
collagen, type IX, alpha 2 |
| Synonyms |
Col9a-2 |
| MMRRC Submission |
040853-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4067 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
120896763-120912522 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 120909586 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 415
(I415N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000030372
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030372]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000030372
AA Change: I415N
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000030372
Gene: ENSMUSG00000028626
AA Change: I415N
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
22 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
24 |
82 |
7.3e-12 |
PFAM |
|
Pfam:Collagen
|
59 |
115 |
2.4e-10 |
PFAM |
|
Pfam:Collagen
|
113 |
170 |
2e-8 |
PFAM |
|
Pfam:Collagen
|
176 |
236 |
8.9e-11 |
PFAM |
|
low complexity region
|
258 |
277 |
N/A |
INTRINSIC |
|
low complexity region
|
288 |
315 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
357 |
435 |
4.4e-8 |
PFAM |
|
Pfam:Collagen
|
459 |
523 |
6.1e-11 |
PFAM |
|
Pfam:Collagen
|
548 |
610 |
4.5e-11 |
PFAM |
|
low complexity region
|
639 |
661 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140119
|
| Meta Mutation Damage Score |
0.1735 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.8%
|
| Validation Efficiency |
98% (61/62) |
| 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. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 58 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700025G04Rik |
T |
A |
1: 151,769,150 (GRCm39) |
T121S |
possibly damaging |
Het |
| 4930503E14Rik |
T |
C |
14: 44,406,641 (GRCm39) |
E136G |
probably damaging |
Het |
| Adgrg4 |
A |
G |
X: 56,005,320 (GRCm39) |
N2527S |
probably damaging |
Het |
| Ak1 |
G |
A |
2: 32,519,593 (GRCm39) |
S7N |
probably benign |
Het |
| Aktip |
A |
C |
8: 91,852,466 (GRCm39) |
I230R |
possibly damaging |
Het |
| Alms1 |
A |
G |
6: 85,598,271 (GRCm39) |
I1032M |
probably damaging |
Het |
| Asb4 |
T |
A |
6: 5,423,651 (GRCm39) |
V266E |
probably damaging |
Het |
| Bace1 |
G |
A |
9: 45,765,962 (GRCm39) |
V130M |
probably damaging |
Het |
| Bglap |
A |
T |
3: 88,291,744 (GRCm39) |
|
probably benign |
Het |
| Brpf3 |
T |
C |
17: 29,040,233 (GRCm39) |
S885P |
probably benign |
Het |
| Chd9 |
A |
T |
8: 91,750,202 (GRCm39) |
I1742F |
possibly damaging |
Het |
| Cybc1 |
A |
T |
11: 121,115,528 (GRCm39) |
|
probably null |
Het |
| Dnajc7 |
T |
C |
11: 100,492,607 (GRCm39) |
Y38C |
probably benign |
Het |
| Dync2i2 |
A |
G |
2: 29,922,820 (GRCm39) |
L309P |
probably benign |
Het |
| Enam |
A |
G |
5: 88,651,236 (GRCm39) |
Y840C |
probably damaging |
Het |
| Etnppl |
T |
A |
3: 130,425,442 (GRCm39) |
C416S |
probably damaging |
Het |
| Fgf20 |
A |
T |
8: 40,732,896 (GRCm39) |
S181T |
probably benign |
Het |
| Fut8 |
T |
A |
12: 77,510,835 (GRCm39) |
Y421N |
probably damaging |
Het |
| Gcn1 |
T |
G |
5: 115,737,147 (GRCm39) |
L1295R |
probably damaging |
Het |
| Gm11437 |
A |
G |
11: 84,055,337 (GRCm39) |
V93A |
probably benign |
Het |
| Gm9989 |
T |
C |
3: 81,829,549 (GRCm39) |
|
noncoding transcript |
Het |
| Gsdmc4 |
A |
T |
15: 63,765,736 (GRCm39) |
|
probably null |
Het |
| Gvin3 |
T |
A |
7: 106,198,772 (GRCm39) |
|
noncoding transcript |
Het |
| Ighv10-1 |
A |
T |
12: 114,442,643 (GRCm39) |
M114K |
probably benign |
Het |
| Il22b |
T |
C |
10: 118,126,115 (GRCm39) |
I161V |
probably damaging |
Het |
| Itfg2 |
T |
A |
6: 128,387,413 (GRCm39) |
|
probably benign |
Het |
| Kirrel1 |
G |
A |
3: 86,995,774 (GRCm39) |
Q387* |
probably null |
Het |
| Klk1 |
C |
T |
7: 43,876,968 (GRCm39) |
R24* |
probably null |
Het |
| Klra7 |
T |
C |
6: 130,208,612 (GRCm39) |
|
probably null |
Het |
| Ltn1 |
T |
C |
16: 87,213,118 (GRCm39) |
Y481C |
possibly damaging |
Het |
| Man1c1 |
G |
C |
4: 134,430,749 (GRCm39) |
P11R |
probably damaging |
Het |
| Mrps2 |
A |
G |
2: 28,359,782 (GRCm39) |
N213S |
probably benign |
Het |
| Muc4 |
A |
T |
16: 32,569,869 (GRCm39) |
I310F |
possibly damaging |
Het |
| Ntrk3 |
T |
A |
7: 78,167,185 (GRCm39) |
Y102F |
probably damaging |
Het |
| Or8k24 |
A |
T |
2: 86,216,431 (GRCm39) |
C110* |
probably null |
Het |
| Otof |
C |
T |
5: 30,556,635 (GRCm39) |
G282D |
probably damaging |
Het |
| Pcdhb2 |
A |
T |
18: 37,430,367 (GRCm39) |
|
probably null |
Het |
| Pign |
A |
T |
1: 105,515,703 (GRCm39) |
|
probably null |
Het |
| Plekha6 |
G |
A |
1: 133,222,416 (GRCm39) |
E1001K |
probably benign |
Het |
| Plxna2 |
C |
T |
1: 194,431,625 (GRCm39) |
S538F |
probably damaging |
Het |
| Ppm1d |
A |
G |
11: 85,236,678 (GRCm39) |
T486A |
probably benign |
Het |
| Pudp |
A |
G |
18: 50,701,329 (GRCm39) |
F135L |
probably benign |
Het |
| Rd3l |
T |
G |
12: 111,945,945 (GRCm39) |
N178T |
probably benign |
Het |
| Rel |
A |
C |
11: 23,703,215 (GRCm39) |
|
probably null |
Het |
| Sf3a1 |
T |
A |
11: 4,117,824 (GRCm39) |
F195L |
probably damaging |
Het |
| Slc30a1 |
G |
C |
1: 191,639,401 (GRCm39) |
A95P |
probably damaging |
Het |
| Slc47a2 |
T |
C |
11: 61,194,773 (GRCm39) |
T469A |
probably benign |
Het |
| Slc4a10 |
A |
T |
2: 61,876,989 (GRCm39) |
M1L |
probably benign |
Het |
| Slc8a1 |
T |
A |
17: 81,955,703 (GRCm39) |
D445V |
probably damaging |
Het |
| Slc9a7 |
C |
T |
X: 20,071,793 (GRCm39) |
G113R |
probably damaging |
Het |
| Spata31e5 |
T |
A |
1: 28,816,712 (GRCm39) |
D440V |
probably damaging |
Het |
| Spic |
T |
C |
10: 88,511,545 (GRCm39) |
H237R |
possibly damaging |
Het |
| Stk26 |
A |
G |
X: 49,977,910 (GRCm39) |
E317G |
probably benign |
Het |
| Tex10 |
A |
T |
4: 48,459,355 (GRCm39) |
Y506* |
probably null |
Het |
| Trhde |
T |
A |
10: 114,280,585 (GRCm39) |
R848* |
probably null |
Het |
| Trpc5 |
T |
A |
X: 143,202,594 (GRCm39) |
R545* |
probably null |
Het |
| Usp24 |
C |
T |
4: 106,216,286 (GRCm39) |
T379M |
possibly damaging |
Het |
| Zfp783 |
A |
T |
6: 47,922,499 (GRCm39) |
|
noncoding transcript |
Het |
|
| Other mutations in Col9a2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01331:Col9a2
|
APN |
4 |
120,902,389 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL01978:Col9a2
|
APN |
4 |
120,901,863 (GRCm39) |
missense |
unknown |
|
|
IGL01995:Col9a2
|
APN |
4 |
120,907,607 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02162:Col9a2
|
APN |
4 |
120,911,531 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02931:Col9a2
|
APN |
4 |
120,910,389 (GRCm39) |
missense |
probably benign |
0.06 |
|
collision
|
UTSW |
4 |
120,906,913 (GRCm39) |
critical splice donor site |
probably null |
|
|
gravity_wave
|
UTSW |
4 |
120,901,216 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0208:Col9a2
|
UTSW |
4 |
120,909,485 (GRCm39) |
splice site |
probably benign |
|
|
R0426:Col9a2
|
UTSW |
4 |
120,901,857 (GRCm39) |
splice site |
probably benign |
|
|
R0512:Col9a2
|
UTSW |
4 |
120,911,504 (GRCm39) |
missense |
probably benign |
0.22 |
|
R0973:Col9a2
|
UTSW |
4 |
120,896,985 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1023:Col9a2
|
UTSW |
4 |
120,901,207 (GRCm39) |
missense |
unknown |
|
|
R1657:Col9a2
|
UTSW |
4 |
120,898,171 (GRCm39) |
missense |
unknown |
|
|
R1724:Col9a2
|
UTSW |
4 |
120,911,099 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2171:Col9a2
|
UTSW |
4 |
120,902,198 (GRCm39) |
nonsense |
probably null |
|
|
R2206:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2221:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2223:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2273:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2274:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2275:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2354:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2392:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2393:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2394:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3421:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3426:Col9a2
|
UTSW |
4 |
120,907,604 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R3710:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3821:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3838:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3839:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4298:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4299:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4595:Col9a2
|
UTSW |
4 |
120,902,352 (GRCm39) |
missense |
probably benign |
0.04 |
|
R4942:Col9a2
|
UTSW |
4 |
120,910,316 (GRCm39) |
missense |
possibly damaging |
0.73 |
|
R5120:Col9a2
|
UTSW |
4 |
120,896,969 (GRCm39) |
missense |
unknown |
|
|
R5434:Col9a2
|
UTSW |
4 |
120,898,162 (GRCm39) |
nonsense |
probably null |
|
|
R6143:Col9a2
|
UTSW |
4 |
120,911,060 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7027:Col9a2
|
UTSW |
4 |
120,901,216 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7056:Col9a2
|
UTSW |
4 |
120,906,913 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7417:Col9a2
|
UTSW |
4 |
120,911,489 (GRCm39) |
missense |
not run |
|
|
R7571:Col9a2
|
UTSW |
4 |
120,896,981 (GRCm39) |
missense |
unknown |
|
|
R9120:Col9a2
|
UTSW |
4 |
120,900,951 (GRCm39) |
splice site |
probably benign |
|
|
R9341:Col9a2
|
UTSW |
4 |
120,911,483 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9343:Col9a2
|
UTSW |
4 |
120,911,483 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9389:Col9a2
|
UTSW |
4 |
120,911,948 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9527:Col9a2
|
UTSW |
4 |
120,899,528 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9620:Col9a2
|
UTSW |
4 |
120,910,403 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9784:Col9a2
|
UTSW |
4 |
120,898,226 (GRCm39) |
missense |
unknown |
|
|
Z1176:Col9a2
|
UTSW |
4 |
120,910,994 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GTCCCGCCTCATGTAAAAGG -3'
(R):5'- TGTCGTGAAATGTCCTTTCCAAG -3'
Sequencing Primer
(F):5'- TCATGTAAAAGGCTGGCCCTG -3'
(R):5'- ATGTCCTTTCCAAGAAGGGAGCTC -3'
|
| Posted On |
2015-05-15 |
Incidental Mutation