Incidental Mutation 'R7056:Col9a2'
| ID |
547908 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a2
|
| Ensembl Gene |
ENSMUSG00000028626 |
| Gene Name |
collagen, type IX, alpha 2 |
| Synonyms |
Col9a-2 |
| MMRRC Submission |
045153-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R7056 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
121039385-121055322 bp(+) (GRCm38) |
| Type of Mutation |
critical splice donor site (1 bp from exon) |
| DNA Base Change (assembly) |
G to A
at 121049716 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000030372
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030372]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably null
Transcript: ENSMUST00000030372
|
| SMART Domains |
Protein: ENSMUSP00000030372
Gene: ENSMUSG00000028626
| 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 |
|
| Meta Mutation Damage Score |
0.9591 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
100% (62/62) |
| 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: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Atr |
T |
A |
9: 95,862,863 (GRCm38) |
S78T |
probably damaging |
Het |
| B2m |
T |
C |
2: 122,150,984 (GRCm38) |
L60P |
probably damaging |
Het |
| C1ra |
G |
A |
6: 124,517,725 (GRCm38) |
E316K |
probably benign |
Het |
| Cep350 |
A |
C |
1: 155,848,627 (GRCm38) |
I3075S |
probably damaging |
Het |
| Cep97 |
A |
G |
16: 55,905,572 (GRCm38) |
S651P |
probably damaging |
Het |
| Chrna5 |
C |
T |
9: 54,981,701 (GRCm38) |
|
probably benign |
Het |
| Cog5 |
T |
C |
12: 31,665,469 (GRCm38) |
V80A |
possibly damaging |
Het |
| Cop1 |
C |
T |
1: 159,250,077 (GRCm38) |
L161F |
probably damaging |
Het |
| Cyp4f17 |
A |
T |
17: 32,527,872 (GRCm38) |
M383L |
possibly damaging |
Het |
| Dennd4a |
A |
G |
9: 64,906,923 (GRCm38) |
D1474G |
possibly damaging |
Het |
| Dgkb |
A |
C |
12: 38,100,493 (GRCm38) |
S100R |
probably benign |
Het |
| Dnah17 |
A |
G |
11: 118,125,386 (GRCm38) |
V309A |
probably benign |
Het |
| Dner |
C |
A |
1: 84,580,736 (GRCm38) |
R169L |
possibly damaging |
Het |
| Dus1l |
T |
C |
11: 120,791,294 (GRCm38) |
E362G |
probably benign |
Het |
| Eed |
A |
T |
7: 89,970,356 (GRCm38) |
S168T |
possibly damaging |
Het |
| Eif3a |
T |
A |
19: 60,763,062 (GRCm38) |
|
probably null |
Het |
| Fam234b |
A |
G |
6: 135,228,452 (GRCm38) |
S472G |
probably benign |
Het |
| Fbn2 |
T |
A |
18: 58,076,726 (GRCm38) |
T1028S |
probably benign |
Het |
| Fbxw16 |
A |
G |
9: 109,436,284 (GRCm38) |
V393A |
possibly damaging |
Het |
| Fig4 |
A |
T |
10: 41,220,932 (GRCm38) |
L838Q |
probably benign |
Het |
| Gm13941 |
T |
G |
2: 111,096,802 (GRCm38) |
S137R |
unknown |
Het |
| Gm9938 |
T |
G |
19: 23,724,617 (GRCm38) |
|
probably benign |
Het |
| Igsf10 |
T |
G |
3: 59,331,080 (GRCm38) |
D560A |
probably damaging |
Het |
| Lrrk2 |
T |
A |
15: 91,774,995 (GRCm38) |
L1870* |
probably null |
Het |
| Mep1b |
T |
A |
18: 21,091,190 (GRCm38) |
Y347N |
probably damaging |
Het |
| Mepce |
T |
C |
5: 137,782,706 (GRCm38) |
N613D |
probably damaging |
Het |
| Mgat3 |
T |
G |
15: 80,211,896 (GRCm38) |
L308R |
probably damaging |
Het |
| Morc2a |
A |
G |
11: 3,675,925 (GRCm38) |
Y175C |
probably damaging |
Het |
| Necab2 |
A |
G |
8: 119,452,139 (GRCm38) |
N98S |
probably benign |
Het |
| Net1 |
T |
C |
13: 3,884,845 (GRCm38) |
M394V |
probably benign |
Het |
| Nfat5 |
G |
A |
8: 107,368,106 (GRCm38) |
G993D |
probably damaging |
Het |
| Obscn |
C |
A |
11: 58,996,296 (GRCm38) |
|
probably benign |
Het |
| Olfr1313 |
T |
C |
2: 112,072,317 (GRCm38) |
N89D |
probably benign |
Het |
| Olfr324 |
A |
G |
11: 58,598,218 (GRCm38) |
Y274C |
probably damaging |
Het |
| Olr1 |
T |
C |
6: 129,488,941 (GRCm38) |
H34R |
probably damaging |
Het |
| Pmm2 |
T |
A |
16: 8,642,764 (GRCm38) |
F27L |
probably damaging |
Het |
| Ptpdc1 |
C |
A |
13: 48,586,990 (GRCm38) |
V261F |
possibly damaging |
Het |
| Pyroxd1 |
G |
T |
6: 142,359,082 (GRCm38) |
R345L |
probably benign |
Het |
| Radil |
A |
T |
5: 142,494,354 (GRCm38) |
C670* |
probably null |
Het |
| Rasgrf2 |
C |
T |
13: 92,030,695 (GRCm38) |
S290N |
probably damaging |
Het |
| Rbm33 |
T |
C |
5: 28,394,003 (GRCm38) |
|
probably benign |
Het |
| Rnf111 |
A |
T |
9: 70,453,675 (GRCm38) |
S501R |
possibly damaging |
Het |
| Sel1l2 |
T |
A |
2: 140,245,414 (GRCm38) |
I446F |
probably benign |
Het |
| Sh3pxd2b |
T |
C |
11: 32,422,737 (GRCm38) |
S635P |
probably benign |
Het |
| Slc30a2 |
G |
A |
4: 134,347,415 (GRCm38) |
R161Q |
probably damaging |
Het |
| Smg1 |
T |
C |
7: 118,146,400 (GRCm38) |
|
probably benign |
Het |
| Sorcs2 |
C |
A |
5: 36,068,130 (GRCm38) |
D132Y |
probably damaging |
Het |
| Sox18 |
T |
C |
2: 181,671,487 (GRCm38) |
D12G |
probably damaging |
Het |
| Srsf4 |
G |
T |
4: 131,900,693 (GRCm38) |
|
probably benign |
Het |
| Susd4 |
C |
A |
1: 182,833,156 (GRCm38) |
T81N |
probably benign |
Het |
| Tmem256 |
G |
T |
11: 69,838,590 (GRCm38) |
|
probably benign |
Het |
| Tor4a |
T |
C |
2: 25,194,841 (GRCm38) |
H350R |
probably benign |
Het |
| Ugt2a3 |
T |
A |
5: 87,337,094 (GRCm38) |
S24C |
probably damaging |
Het |
| Vmn2r111 |
T |
C |
17: 22,559,051 (GRCm38) |
N549S |
possibly damaging |
Het |
| Vmn2r77 |
C |
T |
7: 86,801,815 (GRCm38) |
T303I |
probably benign |
Het |
| Wdr70 |
T |
A |
15: 7,884,396 (GRCm38) |
I591F |
possibly damaging |
Het |
| Wdr93 |
T |
C |
7: 79,749,340 (GRCm38) |
I74T |
probably damaging |
Het |
| Zfp292 |
A |
T |
4: 34,809,784 (GRCm38) |
C1087S |
probably damaging |
Het |
| Zfp592 |
T |
A |
7: 81,023,319 (GRCm38) |
D10E |
probably damaging |
Het |
| Zfp69 |
A |
G |
4: 120,931,098 (GRCm38) |
V340A |
probably benign |
Het |
| Zswim2 |
C |
T |
2: 83,920,748 (GRCm38) |
|
probably null |
Het |
|
| Other mutations in Col9a2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01331:Col9a2
|
APN |
4 |
121,045,192 (GRCm38) |
missense |
possibly damaging |
0.95 |
|
IGL01978:Col9a2
|
APN |
4 |
121,044,666 (GRCm38) |
missense |
unknown |
|
|
IGL01995:Col9a2
|
APN |
4 |
121,050,410 (GRCm38) |
critical splice donor site |
probably null |
|
|
IGL02162:Col9a2
|
APN |
4 |
121,054,334 (GRCm38) |
unclassified |
probably benign |
|
|
IGL02931:Col9a2
|
APN |
4 |
121,053,192 (GRCm38) |
missense |
probably benign |
0.06 |
|
collision
|
UTSW |
4 |
121,049,716 (GRCm38) |
critical splice donor site |
probably null |
|
|
gravity_wave
|
UTSW |
4 |
121,044,019 (GRCm38) |
critical splice donor site |
probably null |
|
|
R0208:Col9a2
|
UTSW |
4 |
121,052,288 (GRCm38) |
splice site |
probably benign |
|
|
R0426:Col9a2
|
UTSW |
4 |
121,044,660 (GRCm38) |
splice site |
probably benign |
|
|
R0512:Col9a2
|
UTSW |
4 |
121,054,307 (GRCm38) |
missense |
probably benign |
0.22 |
|
R0973:Col9a2
|
UTSW |
4 |
121,039,788 (GRCm38) |
critical splice donor site |
probably null |
|
|
R1023:Col9a2
|
UTSW |
4 |
121,044,010 (GRCm38) |
missense |
unknown |
|
|
R1657:Col9a2
|
UTSW |
4 |
121,040,974 (GRCm38) |
missense |
unknown |
|
|
R1724:Col9a2
|
UTSW |
4 |
121,053,902 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R2171:Col9a2
|
UTSW |
4 |
121,045,001 (GRCm38) |
nonsense |
probably null |
|
|
R2206:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2221:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2223:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2273:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2274:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2275:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2354:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2392:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2393:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R2394:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R3421:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R3426:Col9a2
|
UTSW |
4 |
121,050,407 (GRCm38) |
missense |
possibly damaging |
0.93 |
|
R3710:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R3821:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R3838:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R3839:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R4067:Col9a2
|
UTSW |
4 |
121,052,389 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4298:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R4299:Col9a2
|
UTSW |
4 |
121,054,258 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R4595:Col9a2
|
UTSW |
4 |
121,045,155 (GRCm38) |
missense |
probably benign |
0.04 |
|
R4942:Col9a2
|
UTSW |
4 |
121,053,119 (GRCm38) |
missense |
possibly damaging |
0.73 |
|
R5120:Col9a2
|
UTSW |
4 |
121,039,772 (GRCm38) |
missense |
unknown |
|
|
R5434:Col9a2
|
UTSW |
4 |
121,040,965 (GRCm38) |
nonsense |
probably null |
|
|
R6143:Col9a2
|
UTSW |
4 |
121,053,863 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R7027:Col9a2
|
UTSW |
4 |
121,044,019 (GRCm38) |
critical splice donor site |
probably null |
|
|
R7417:Col9a2
|
UTSW |
4 |
121,054,292 (GRCm38) |
missense |
not run |
|
|
R7571:Col9a2
|
UTSW |
4 |
121,039,784 (GRCm38) |
missense |
unknown |
|
|
R9120:Col9a2
|
UTSW |
4 |
121,043,754 (GRCm38) |
splice site |
probably benign |
|
|
R9341:Col9a2
|
UTSW |
4 |
121,054,286 (GRCm38) |
missense |
probably benign |
0.03 |
|
R9343:Col9a2
|
UTSW |
4 |
121,054,286 (GRCm38) |
missense |
probably benign |
0.03 |
|
R9389:Col9a2
|
UTSW |
4 |
121,054,751 (GRCm38) |
missense |
probably benign |
0.00 |
|
R9527:Col9a2
|
UTSW |
4 |
121,042,331 (GRCm38) |
critical splice donor site |
probably null |
|
|
R9620:Col9a2
|
UTSW |
4 |
121,053,206 (GRCm38) |
critical splice donor site |
probably null |
|
|
R9784:Col9a2
|
UTSW |
4 |
121,041,029 (GRCm38) |
missense |
unknown |
|
|
Z1176:Col9a2
|
UTSW |
4 |
121,053,797 (GRCm38) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- CATTATTATCGGAACTGGAGAAAGC -3'
(R):5'- GTGTGTGGATGACCGCTAAG -3'
Sequencing Primer
(F):5'- GATTCCAGTCAGCCTCTGAG -3'
(R):5'- GACCGCTAAGATTGTTCAAGC -3'
|
| Posted On |
2019-05-13 |
Incidental Mutation