Incidental Mutation 'R9343:Col2a1'
| ID |
715998 |
| 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 |
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R9343 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
15 |
| Chromosomal Location |
97873483-97902525 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 97877775 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 1049
(D1049G)
|
| 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 damaging
Transcript: ENSMUST00000023123
AA Change: D1049G
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000023123
Gene: ENSMUSG00000022483
AA Change: D1049G
| 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 damaging
Transcript: ENSMUST00000088355
AA Change: D981G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000085693
Gene: ENSMUSG00000022483
AA Change: D981G
| 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: 99.9%
- 10x: 99.6%
- 20x: 98.7%
|
| Validation Efficiency |
100% (45/45) |
| 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: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abtb2 |
A |
G |
2: 103,547,505 (GRCm39) |
I960V |
probably benign |
Het |
| Alpk3 |
A |
G |
7: 80,742,079 (GRCm39) |
D632G |
probably benign |
Het |
| Aplp2 |
A |
T |
9: 31,122,935 (GRCm39) |
L30Q |
unknown |
Het |
| Axl |
A |
T |
7: 25,473,544 (GRCm39) |
Y361N |
probably damaging |
Het |
| Brinp2 |
A |
T |
1: 158,077,090 (GRCm39) |
|
probably benign |
Het |
| Bsn |
T |
C |
9: 107,992,701 (GRCm39) |
D1017G |
probably damaging |
Het |
| Cc2d2a |
A |
T |
5: 43,875,999 (GRCm39) |
D1046V |
probably damaging |
Het |
| Cdc42bpg |
G |
A |
19: 6,364,553 (GRCm39) |
G594S |
probably damaging |
Het |
| Clcn6 |
A |
G |
4: 148,098,458 (GRCm39) |
S519P |
probably benign |
Het |
| Cnot2 |
T |
G |
10: 116,346,326 (GRCm39) |
H92P |
|
Het |
| Creld1 |
C |
T |
6: 113,466,728 (GRCm39) |
A237V |
probably benign |
Het |
| Csf2rb2 |
A |
T |
15: 78,171,287 (GRCm39) |
|
probably benign |
Het |
| Csmd3 |
G |
A |
15: 48,015,001 (GRCm39) |
T643I |
probably damaging |
Het |
| Fam186b |
G |
A |
15: 99,177,616 (GRCm39) |
A570V |
probably damaging |
Het |
| Fcmr |
A |
T |
1: 130,802,072 (GRCm39) |
T109S |
|
Het |
| Grap |
C |
A |
11: 61,562,551 (GRCm39) |
P174Q |
possibly damaging |
Het |
| Itgb5 |
T |
A |
16: 33,730,826 (GRCm39) |
|
probably benign |
Het |
| Kidins220 |
A |
G |
12: 25,058,078 (GRCm39) |
N561S |
probably damaging |
Het |
| Mri1 |
A |
T |
8: 84,983,796 (GRCm39) |
S32T |
probably benign |
Het |
| Mrtfb |
T |
C |
16: 13,218,791 (GRCm39) |
V479A |
probably benign |
Het |
| Muc4 |
A |
T |
16: 32,569,971 (GRCm39) |
T344S |
possibly damaging |
Het |
| Npc1 |
A |
G |
18: 12,334,769 (GRCm39) |
I661T |
possibly damaging |
Het |
| Npy1r |
A |
G |
8: 67,156,751 (GRCm39) |
N57S |
probably damaging |
Het |
| Pds5b |
A |
G |
5: 150,704,186 (GRCm39) |
D863G |
probably damaging |
Het |
| Phf14 |
T |
A |
6: 11,961,563 (GRCm39) |
V400D |
probably damaging |
Het |
| Polr2l |
A |
G |
7: 141,053,246 (GRCm39) |
I56T |
probably benign |
Het |
| Ppat |
A |
G |
5: 77,063,884 (GRCm39) |
I422T |
probably benign |
Het |
| Prkcg |
T |
A |
7: 3,359,124 (GRCm39) |
S110R |
possibly damaging |
Het |
| Rab7b |
A |
T |
1: 131,639,540 (GRCm39) |
|
probably benign |
Het |
| Rnf152 |
A |
T |
1: 105,212,251 (GRCm39) |
L102Q |
|
Het |
| Samd12 |
A |
G |
15: 53,583,088 (GRCm39) |
V82A |
probably damaging |
Het |
| Serpina1e |
T |
A |
12: 103,917,299 (GRCm39) |
R123S |
probably benign |
Het |
| Slit1 |
T |
A |
19: 41,615,737 (GRCm39) |
N794I |
probably damaging |
Het |
| Surf6 |
T |
C |
2: 26,783,006 (GRCm39) |
K154R |
probably damaging |
Het |
| Tln2 |
C |
T |
9: 67,230,353 (GRCm39) |
A71T |
probably benign |
Het |
| Trim3 |
A |
G |
7: 105,260,673 (GRCm39) |
Y649H |
probably benign |
Het |
| Ttll7 |
T |
A |
3: 146,667,497 (GRCm39) |
W808R |
probably damaging |
Het |
| Tvp23a |
T |
C |
16: 10,245,287 (GRCm39) |
D104G |
probably damaging |
Het |
| Upp2 |
A |
G |
2: 58,645,339 (GRCm39) |
|
probably benign |
Het |
| Vipr1 |
G |
A |
9: 121,471,993 (GRCm39) |
|
probably null |
Het |
| Vmn1r119 |
A |
G |
7: 20,746,358 (GRCm39) |
V8A |
probably benign |
Het |
| Vmn1r209 |
T |
A |
13: 22,990,546 (GRCm39) |
H48L |
probably damaging |
Het |
| Wdr11 |
T |
C |
7: 129,232,523 (GRCm39) |
|
probably null |
Het |
| Zcchc17 |
T |
C |
4: 130,210,546 (GRCm39) |
D207G |
probably damaging |
Het |
| Zfp78 |
T |
C |
7: 6,381,942 (GRCm39) |
S331P |
probably damaging |
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 |
|
|
R7872:Col2a1
|
UTSW |
15 |
97,898,458 (GRCm39) |
nonsense |
probably null |
|
|
R8177:Col2a1
|
UTSW |
15 |
97,874,654 (GRCm39) |
missense |
unknown |
|
|
R8306:Col2a1
|
UTSW |
15 |
97,888,849 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
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'- TCACCACGATCTCCCTGTAG -3'
(R):5'- TTGTCTGCATCCTTTCAGGG -3'
Sequencing Primer
(F):5'- TCCCTGTAGGAGCAAAGTGTC -3'
(R):5'- TGGAGACAGAGGTCCTCCTG -3'
|
| Posted On |
2022-06-15 |
Incidental Mutation