Incidental Mutation 'R7872:Col2a1'
ID |
608204 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col2a1
|
Ensembl Gene |
ENSMUSG00000022483 |
Gene Name |
collagen, type II, alpha 1 |
Synonyms |
Rgsc413, M100413, Rgsc856, Col2a-1, M100856, Del1, Col2a, Col2, Lpk |
MMRRC Submission |
045924-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R7872 (G1)
|
Quality Score |
225.009 |
Status
|
Not validated
|
Chromosome |
15 |
Chromosomal Location |
97873483-97902525 bp(-) (GRCm39) |
Type of Mutation |
nonsense |
DNA Base Change (assembly) |
G to A
at 97898458 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Glutamine to Stop codon
at position 39
(Q39*)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000023123
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000023123]
[ENSMUST00000088355]
|
AlphaFold |
P28481 |
PDB Structure |
ANTI CITRULLINATED COLLAGEN TYPE 2 ANTIBODY ACC4 IN COMPLEX WITH A CITRULLINATED PEPTIDE [X-RAY DIFFRACTION]
Crystal structure of the arthritogenic antibody M2139 (Fab fragment) in complex with the triple-helical J1 peptide [X-RAY DIFFRACTION]
|
Predicted Effect |
probably null
Transcript: ENSMUST00000023123
AA Change: Q39*
|
SMART Domains |
Protein: ENSMUSP00000023123 Gene: ENSMUSG00000022483 AA Change: Q39*
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
VWC
|
34 |
88 |
1.59e-21 |
SMART |
Pfam:Collagen
|
115 |
175 |
1.3e-11 |
PFAM |
Pfam:Collagen
|
199 |
260 |
7.2e-11 |
PFAM |
Pfam:Collagen
|
258 |
317 |
1.3e-12 |
PFAM |
Pfam:Collagen
|
312 |
377 |
4e-9 |
PFAM |
low complexity region
|
395 |
411 |
N/A |
INTRINSIC |
low complexity region
|
416 |
451 |
N/A |
INTRINSIC |
internal_repeat_5
|
456 |
468 |
5.45e-5 |
PROSPERO |
low complexity region
|
471 |
513 |
N/A |
INTRINSIC |
internal_repeat_3
|
516 |
619 |
3.99e-13 |
PROSPERO |
internal_repeat_1
|
524 |
567 |
1.6e-17 |
PROSPERO |
low complexity region
|
621 |
633 |
N/A |
INTRINSIC |
low complexity region
|
636 |
655 |
N/A |
INTRINSIC |
low complexity region
|
659 |
687 |
N/A |
INTRINSIC |
low complexity region
|
696 |
753 |
N/A |
INTRINSIC |
internal_repeat_5
|
756 |
768 |
5.45e-5 |
PROSPERO |
low complexity region
|
783 |
804 |
N/A |
INTRINSIC |
Pfam:Collagen
|
852 |
918 |
1.1e-8 |
PFAM |
Pfam:Collagen
|
876 |
941 |
1.9e-9 |
PFAM |
Pfam:Collagen
|
900 |
966 |
2.4e-9 |
PFAM |
Pfam:Collagen
|
983 |
1049 |
2.1e-10 |
PFAM |
low complexity region
|
1062 |
1081 |
N/A |
INTRINSIC |
Pfam:Collagen
|
1101 |
1172 |
3.4e-9 |
PFAM |
Pfam:Collagen
|
1158 |
1218 |
1.3e-9 |
PFAM |
COLFI
|
1252 |
1487 |
3.06e-184 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000088355
|
SMART Domains |
Protein: ENSMUSP00000085693 Gene: ENSMUSG00000022483
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
Pfam:Collagen
|
47 |
107 |
1.2e-11 |
PFAM |
Pfam:Collagen
|
131 |
192 |
7.2e-11 |
PFAM |
Pfam:Collagen
|
190 |
249 |
1.3e-12 |
PFAM |
low complexity region
|
262 |
314 |
N/A |
INTRINSIC |
Pfam:Collagen
|
327 |
405 |
3.5e-7 |
PFAM |
Pfam:Collagen
|
361 |
429 |
7.6e-10 |
PFAM |
internal_repeat_3
|
448 |
551 |
1.3e-13 |
PROSPERO |
internal_repeat_7
|
454 |
466 |
2.86e-5 |
PROSPERO |
internal_repeat_1
|
456 |
499 |
4.05e-18 |
PROSPERO |
internal_repeat_6
|
481 |
504 |
1.7e-5 |
PROSPERO |
low complexity region
|
553 |
565 |
N/A |
INTRINSIC |
low complexity region
|
568 |
587 |
N/A |
INTRINSIC |
low complexity region
|
591 |
619 |
N/A |
INTRINSIC |
low complexity region
|
628 |
685 |
N/A |
INTRINSIC |
internal_repeat_4
|
688 |
712 |
8.3e-12 |
PROSPERO |
low complexity region
|
715 |
736 |
N/A |
INTRINSIC |
low complexity region
|
747 |
784 |
N/A |
INTRINSIC |
Pfam:Collagen
|
808 |
878 |
9.8e-9 |
PFAM |
Pfam:Collagen
|
832 |
898 |
2.1e-9 |
PFAM |
Pfam:Collagen
|
916 |
979 |
7.2e-10 |
PFAM |
Pfam:Collagen
|
937 |
1005 |
2.1e-8 |
PFAM |
Pfam:Collagen
|
973 |
1049 |
6e-7 |
PFAM |
Pfam:Collagen
|
1030 |
1094 |
1.5e-10 |
PFAM |
Pfam:Collagen
|
1088 |
1150 |
1.4e-9 |
PFAM |
COLFI
|
1184 |
1419 |
3.06e-184 |
SMART |
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.0%
|
Validation Efficiency |
|
MGI Phenotype |
FUNCTION: This gene encodes the alpha-1 subunit of the fibril-forming type II collagen, the major component of cartilage and the vitreous humor of the eye. The encoded preproprotein forms homotrimeric, triple helical procollagen that undergoes proteolytic processing during fibirl formation. Mice harboring certain mutations in this gene exhibit severe chondrodysplasia characterized by short limbs and trunch, craniofacial deformities and cleft palate. A complete lack of the encoded protein in mice results in postnatal lethality. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Dec 2015] PHENOTYPE: Mutations in this locus affect cartilage development. Homozygotes die perinatally with anomalies such as shortened limbs without epiphiseal growth plates, cleft palate and persistence of notochord. Heterozygotes are dwarfed with reduced cartilage matrix. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 61 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acta2 |
C |
T |
19: 34,220,839 (GRCm39) |
D290N |
probably damaging |
Het |
Adam18 |
T |
C |
8: 25,101,116 (GRCm39) |
D682G |
probably benign |
Het |
Ankrd46 |
A |
G |
15: 36,485,989 (GRCm39) |
V88A |
possibly damaging |
Het |
Ankub1 |
T |
A |
3: 57,572,807 (GRCm39) |
K305I |
probably damaging |
Het |
Atrn |
T |
A |
2: 130,812,147 (GRCm39) |
|
probably null |
Het |
Bambi |
A |
T |
18: 3,511,406 (GRCm39) |
T76S |
probably benign |
Het |
Cacna1a |
T |
A |
8: 85,310,283 (GRCm39) |
V1447E |
probably damaging |
Het |
Calcoco2 |
GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC |
GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC |
11: 95,990,808 (GRCm39) |
|
probably benign |
Het |
Clcn2 |
A |
G |
16: 20,527,210 (GRCm39) |
M629T |
probably damaging |
Het |
Clcn4 |
T |
C |
7: 7,290,780 (GRCm39) |
N673S |
probably benign |
Het |
Col20a1 |
T |
C |
2: 180,628,371 (GRCm39) |
F15S |
probably benign |
Het |
Creb3 |
A |
G |
4: 43,563,332 (GRCm39) |
E119G |
probably benign |
Het |
Dnah5 |
A |
C |
15: 28,245,830 (GRCm39) |
D556A |
probably damaging |
Het |
Edar |
C |
T |
10: 58,446,348 (GRCm39) |
M192I |
possibly damaging |
Het |
Fam91a1 |
A |
G |
15: 58,320,209 (GRCm39) |
M634V |
probably benign |
Het |
Fbxo10 |
C |
T |
4: 45,051,699 (GRCm39) |
V471I |
not run |
Het |
Fer1l5 |
T |
C |
1: 36,460,967 (GRCm39) |
F2032L |
probably benign |
Het |
Gm5150 |
A |
C |
3: 16,060,485 (GRCm39) |
M1R |
probably null |
Het |
Grin1 |
T |
C |
2: 25,188,202 (GRCm39) |
E509G |
probably benign |
Het |
Igkv10-94 |
C |
T |
6: 68,681,913 (GRCm39) |
|
probably benign |
Het |
Il18bp |
A |
G |
7: 101,666,002 (GRCm39) |
Y59H |
possibly damaging |
Het |
Ints8 |
A |
T |
4: 11,254,062 (GRCm39) |
C17S |
probably benign |
Het |
Kcnmb1 |
T |
C |
11: 33,916,275 (GRCm39) |
Y74H |
probably damaging |
Het |
Kpna1 |
T |
C |
16: 35,843,565 (GRCm39) |
V313A |
probably benign |
Het |
Lrp4 |
C |
T |
2: 91,321,061 (GRCm39) |
T1029I |
possibly damaging |
Het |
Lrrc7 |
A |
T |
3: 158,059,099 (GRCm39) |
C3S |
probably damaging |
Het |
Lyst |
C |
A |
13: 13,810,450 (GRCm39) |
H707N |
probably benign |
Het |
Map3k20 |
A |
G |
2: 72,202,098 (GRCm39) |
K148R |
probably damaging |
Het |
Mcidas |
G |
A |
13: 113,135,521 (GRCm39) |
G315S |
probably damaging |
Het |
Miip |
C |
T |
4: 147,947,375 (GRCm39) |
G236S |
probably benign |
Het |
Mocs1 |
T |
A |
17: 49,746,561 (GRCm39) |
I177N |
probably damaging |
Het |
Muc5b |
A |
G |
7: 141,399,850 (GRCm39) |
D441G |
unknown |
Het |
Ncoa1 |
T |
C |
12: 4,328,186 (GRCm39) |
N884S |
probably benign |
Het |
Or12j4 |
A |
G |
7: 140,046,696 (GRCm39) |
N194S |
probably damaging |
Het |
Or51a39 |
A |
G |
7: 102,363,389 (GRCm39) |
V77A |
probably benign |
Het |
Padi6 |
A |
T |
4: 140,455,073 (GRCm39) |
F621L |
probably damaging |
Het |
Pde8b |
C |
A |
13: 95,223,347 (GRCm39) |
M197I |
possibly damaging |
Het |
Pear1 |
T |
A |
3: 87,659,522 (GRCm39) |
I771L |
probably benign |
Het |
Poli |
A |
G |
18: 70,655,891 (GRCm39) |
L281P |
probably damaging |
Het |
Prdm12 |
T |
C |
2: 31,530,231 (GRCm39) |
W41R |
probably damaging |
Het |
Prkdc |
T |
G |
16: 15,532,870 (GRCm39) |
S1500A |
probably benign |
Het |
Prune2 |
T |
A |
19: 17,096,798 (GRCm39) |
H767Q |
probably benign |
Het |
Rasgef1b |
G |
A |
5: 99,382,403 (GRCm39) |
Q196* |
probably null |
Het |
Rnpc3 |
A |
T |
3: 113,416,096 (GRCm39) |
L121* |
probably null |
Het |
Rpp14 |
A |
G |
14: 8,083,724 (GRCm38) |
M1V |
probably null |
Het |
Ryr2 |
T |
A |
13: 11,610,610 (GRCm39) |
D4072V |
probably damaging |
Het |
Sgms1 |
T |
C |
19: 32,102,765 (GRCm39) |
H314R |
probably damaging |
Het |
Six4 |
CT |
C |
12: 73,151,013 (GRCm39) |
|
probably benign |
Het |
Slc37a3 |
A |
T |
6: 39,324,244 (GRCm39) |
Y335N |
probably damaging |
Het |
Tcp11l1 |
A |
T |
2: 104,536,837 (GRCm39) |
H9Q |
probably benign |
Het |
Tnrc6a |
T |
A |
7: 122,779,057 (GRCm39) |
M1256K |
probably damaging |
Het |
Trpc6 |
A |
G |
9: 8,609,910 (GRCm39) |
N126S |
probably damaging |
Het |
Tut4 |
T |
G |
4: 108,374,715 (GRCm39) |
C933G |
probably damaging |
Het |
Ubr4 |
T |
C |
4: 139,120,373 (GRCm39) |
F266S |
possibly damaging |
Het |
Uimc1 |
A |
G |
13: 55,217,550 (GRCm39) |
V424A |
possibly damaging |
Het |
Utrn |
T |
C |
10: 12,573,873 (GRCm39) |
I1066V |
probably benign |
Het |
Vmn1r204 |
A |
G |
13: 22,740,404 (GRCm39) |
T12A |
probably benign |
Het |
Vmn1r57 |
T |
A |
7: 5,223,613 (GRCm39) |
I46N |
possibly damaging |
Het |
Vmn1r91 |
T |
C |
7: 19,835,839 (GRCm39) |
Y253H |
probably benign |
Het |
Vmn2r14 |
T |
A |
5: 109,369,219 (GRCm39) |
H118L |
probably benign |
Het |
Zfp775 |
A |
G |
6: 48,597,404 (GRCm39) |
K426R |
probably benign |
Het |
|
Other mutations in Col2a1 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01025:Col2a1
|
APN |
15 |
97,874,054 (GRCm39) |
missense |
unknown |
|
IGL01286:Col2a1
|
APN |
15 |
97,892,759 (GRCm39) |
missense |
unknown |
|
IGL01369:Col2a1
|
APN |
15 |
97,875,707 (GRCm39) |
missense |
unknown |
|
IGL01747:Col2a1
|
APN |
15 |
97,889,273 (GRCm39) |
splice site |
probably benign |
|
IGL02086:Col2a1
|
APN |
15 |
97,884,618 (GRCm39) |
splice site |
probably null |
|
IGL02549:Col2a1
|
APN |
15 |
97,875,680 (GRCm39) |
missense |
unknown |
|
IGL03289:Col2a1
|
APN |
15 |
97,878,762 (GRCm39) |
missense |
unknown |
|
IGL03369:Col2a1
|
APN |
15 |
97,879,923 (GRCm39) |
missense |
unknown |
|
Foreseen
|
UTSW |
15 |
97,874,674 (GRCm39) |
missense |
unknown |
|
FR4304:Col2a1
|
UTSW |
15 |
97,886,862 (GRCm39) |
splice site |
probably null |
|
FR4340:Col2a1
|
UTSW |
15 |
97,886,862 (GRCm39) |
splice site |
probably null |
|
FR4342:Col2a1
|
UTSW |
15 |
97,886,862 (GRCm39) |
splice site |
probably null |
|
FR4589:Col2a1
|
UTSW |
15 |
97,886,862 (GRCm39) |
splice site |
probably null |
|
LCD18:Col2a1
|
UTSW |
15 |
97,886,862 (GRCm39) |
splice site |
probably null |
|
R0124:Col2a1
|
UTSW |
15 |
97,896,743 (GRCm39) |
missense |
unknown |
|
R0227:Col2a1
|
UTSW |
15 |
97,874,636 (GRCm39) |
missense |
unknown |
|
R0690:Col2a1
|
UTSW |
15 |
97,878,073 (GRCm39) |
missense |
unknown |
|
R1434:Col2a1
|
UTSW |
15 |
97,877,532 (GRCm39) |
missense |
probably damaging |
0.96 |
R1473:Col2a1
|
UTSW |
15 |
97,880,789 (GRCm39) |
splice site |
probably benign |
|
R1577:Col2a1
|
UTSW |
15 |
97,877,083 (GRCm39) |
missense |
probably damaging |
1.00 |
R1598:Col2a1
|
UTSW |
15 |
97,877,131 (GRCm39) |
missense |
probably damaging |
0.99 |
R1837:Col2a1
|
UTSW |
15 |
97,894,522 (GRCm39) |
splice site |
probably benign |
|
R2153:Col2a1
|
UTSW |
15 |
97,885,461 (GRCm39) |
missense |
unknown |
|
R2965:Col2a1
|
UTSW |
15 |
97,873,976 (GRCm39) |
missense |
unknown |
|
R2966:Col2a1
|
UTSW |
15 |
97,873,976 (GRCm39) |
missense |
unknown |
|
R3710:Col2a1
|
UTSW |
15 |
97,888,788 (GRCm39) |
splice site |
probably benign |
|
R3838:Col2a1
|
UTSW |
15 |
97,898,462 (GRCm39) |
intron |
probably benign |
|
R3838:Col2a1
|
UTSW |
15 |
97,886,857 (GRCm39) |
missense |
unknown |
|
R4112:Col2a1
|
UTSW |
15 |
97,881,582 (GRCm39) |
missense |
probably benign |
0.18 |
R4417:Col2a1
|
UTSW |
15 |
97,896,466 (GRCm39) |
missense |
unknown |
|
R4656:Col2a1
|
UTSW |
15 |
97,874,057 (GRCm39) |
missense |
unknown |
|
R4960:Col2a1
|
UTSW |
15 |
97,874,030 (GRCm39) |
missense |
unknown |
|
R5008:Col2a1
|
UTSW |
15 |
97,877,550 (GRCm39) |
missense |
probably benign |
0.28 |
R5435:Col2a1
|
UTSW |
15 |
97,898,391 (GRCm39) |
intron |
probably benign |
|
R5473:Col2a1
|
UTSW |
15 |
97,885,370 (GRCm39) |
missense |
unknown |
|
R6042:Col2a1
|
UTSW |
15 |
97,898,451 (GRCm39) |
intron |
probably benign |
|
R6118:Col2a1
|
UTSW |
15 |
97,896,448 (GRCm39) |
missense |
unknown |
|
R6183:Col2a1
|
UTSW |
15 |
97,886,671 (GRCm39) |
missense |
unknown |
|
R6187:Col2a1
|
UTSW |
15 |
97,886,671 (GRCm39) |
missense |
unknown |
|
R6401:Col2a1
|
UTSW |
15 |
97,883,773 (GRCm39) |
missense |
unknown |
|
R6550:Col2a1
|
UTSW |
15 |
97,874,674 (GRCm39) |
missense |
unknown |
|
R6568:Col2a1
|
UTSW |
15 |
97,875,157 (GRCm39) |
missense |
unknown |
|
R6988:Col2a1
|
UTSW |
15 |
97,902,335 (GRCm39) |
missense |
unknown |
|
R7060:Col2a1
|
UTSW |
15 |
97,874,022 (GRCm39) |
missense |
unknown |
|
R7069:Col2a1
|
UTSW |
15 |
97,896,469 (GRCm39) |
missense |
unknown |
|
R7167:Col2a1
|
UTSW |
15 |
97,898,337 (GRCm39) |
missense |
unknown |
|
R7294:Col2a1
|
UTSW |
15 |
97,885,168 (GRCm39) |
splice site |
probably null |
|
R7392:Col2a1
|
UTSW |
15 |
97,878,032 (GRCm39) |
nonsense |
probably null |
|
R7491:Col2a1
|
UTSW |
15 |
97,874,040 (GRCm39) |
missense |
not run |
|
R7583:Col2a1
|
UTSW |
15 |
97,874,065 (GRCm39) |
missense |
unknown |
|
R7665:Col2a1
|
UTSW |
15 |
97,874,581 (GRCm39) |
missense |
unknown |
|
R8177:Col2a1
|
UTSW |
15 |
97,874,654 (GRCm39) |
missense |
unknown |
|
R8306:Col2a1
|
UTSW |
15 |
97,888,849 (GRCm39) |
critical splice acceptor site |
probably null |
|
R9343:Col2a1
|
UTSW |
15 |
97,877,775 (GRCm39) |
missense |
probably damaging |
0.99 |
R9458:Col2a1
|
UTSW |
15 |
97,876,242 (GRCm39) |
missense |
unknown |
|
Z1177:Col2a1
|
UTSW |
15 |
97,896,226 (GRCm39) |
missense |
unknown |
|
Z1177:Col2a1
|
UTSW |
15 |
97,881,854 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- GCATTTGCTGTGTCTCCGAG -3'
(R):5'- TGTCAGTTCAGCCTGTCTG -3'
Sequencing Primer
(F):5'- TAAATAAATTACGACCACTGGCAG -3'
(R):5'- CAGTTCAGCCTGTCTGGTGTG -3'
|
Posted On |
2019-12-20 |