Incidental Mutation 'R5473:Col2a1'
| ID |
433948 |
| 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 |
043034-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5473 (G1)
|
| Quality Score |
194 |
|
Status
|
Validated
|
| Chromosome |
15 |
| Chromosomal Location |
97873483-97902525 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 97885370 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Aspartic acid
at position 491
(A491D)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000085693
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000023123]
[ENSMUST00000088355]
[ENSMUST00000131560]
|
| AlphaFold |
P28481 |
| Predicted Effect |
unknown
Transcript: ENSMUST00000023123
AA Change: A559D
|
| SMART Domains |
Protein: ENSMUSP00000023123
Gene: ENSMUSG00000022483
AA Change: A559D
| 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 |
unknown
Transcript: ENSMUST00000088355
AA Change: A491D
|
| SMART Domains |
Protein: ENSMUSP00000085693
Gene: ENSMUSG00000022483
AA Change: A491D
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128547
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000131560
|
| SMART Domains |
Protein: ENSMUSP00000116951
Gene: ENSMUSG00000022483
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
|
VWC
|
34 |
88 |
1.59e-21 |
SMART |
|
low complexity region
|
109 |
132 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000131910
|
| Meta Mutation Damage Score |
0.1429 |
| Coding Region Coverage |
- 1x: 98.2%
- 3x: 97.3%
- 10x: 95.2%
- 20x: 90.6%
|
| Validation Efficiency |
100% (66/66) |
| 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: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acsm4 |
T |
C |
7: 119,312,173 (GRCm39) |
Y549H |
probably damaging |
Het |
| Adamtsl4 |
G |
T |
3: 95,587,303 (GRCm39) |
Q758K |
probably damaging |
Het |
| Anapc1 |
G |
T |
2: 128,449,115 (GRCm39) |
|
probably benign |
Het |
| Ankrd26 |
A |
T |
6: 118,492,797 (GRCm39) |
C1316S |
probably benign |
Het |
| Birc5 |
T |
C |
11: 117,743,533 (GRCm39) |
V89A |
possibly damaging |
Het |
| Camk2d |
G |
T |
3: 126,391,048 (GRCm39) |
|
probably benign |
Het |
| Ccdc47 |
A |
T |
11: 106,095,855 (GRCm39) |
S280R |
probably damaging |
Het |
| Cntnap5a |
T |
A |
1: 116,016,986 (GRCm39) |
F193Y |
probably benign |
Het |
| Cntrob |
G |
T |
11: 69,213,579 (GRCm39) |
D70E |
possibly damaging |
Het |
| Col24a1 |
A |
C |
3: 145,243,016 (GRCm39) |
M1519L |
probably benign |
Het |
| Crat |
A |
G |
2: 30,297,726 (GRCm39) |
L266P |
probably damaging |
Het |
| Dlgap1 |
A |
T |
17: 70,824,025 (GRCm39) |
|
probably benign |
Het |
| Dnaaf10 |
T |
C |
11: 17,174,591 (GRCm39) |
V153A |
probably damaging |
Het |
| Eya4 |
T |
A |
10: 23,039,351 (GRCm39) |
H104L |
probably benign |
Het |
| Fam83b |
T |
C |
9: 76,398,782 (GRCm39) |
K774E |
probably damaging |
Het |
| Fgd6 |
T |
C |
10: 93,880,538 (GRCm39) |
I464T |
probably benign |
Het |
| Gorasp2 |
A |
C |
2: 70,508,950 (GRCm39) |
M123L |
probably damaging |
Het |
| H2-M10.3 |
A |
T |
17: 36,678,261 (GRCm39) |
V188E |
probably damaging |
Het |
| Hnrnpk |
A |
T |
13: 58,541,913 (GRCm39) |
W333R |
probably damaging |
Het |
| Hrh4 |
T |
C |
18: 13,154,985 (GRCm39) |
Y175H |
probably benign |
Het |
| Igf2r |
G |
T |
17: 12,914,201 (GRCm39) |
T1756K |
probably benign |
Het |
| Kcnq5 |
A |
G |
1: 21,527,626 (GRCm39) |
|
probably null |
Het |
| Kiz |
G |
T |
2: 146,811,915 (GRCm39) |
E675* |
probably null |
Het |
| Mcm3ap |
T |
G |
10: 76,338,593 (GRCm39) |
L1407R |
probably damaging |
Het |
| Mdc1 |
A |
G |
17: 36,158,952 (GRCm39) |
D444G |
probably benign |
Het |
| Myl3 |
C |
A |
9: 110,597,026 (GRCm39) |
H129N |
probably damaging |
Het |
| Neo1 |
T |
C |
9: 58,788,126 (GRCm39) |
N1309S |
possibly damaging |
Het |
| Nrxn1 |
A |
T |
17: 90,897,520 (GRCm39) |
Y269N |
probably damaging |
Het |
| Nsd1 |
A |
G |
13: 55,395,585 (GRCm39) |
N1165S |
probably damaging |
Het |
| Nuf2 |
T |
C |
1: 169,334,856 (GRCm39) |
D302G |
probably benign |
Het |
| Olfr908 |
A |
G |
9: 38,427,508 (GRCm39) |
Y60C |
probably damaging |
Het |
| Or10j3 |
G |
C |
1: 173,031,732 (GRCm39) |
G270R |
probably benign |
Het |
| Or14j1 |
T |
C |
17: 38,146,630 (GRCm39) |
F247L |
probably benign |
Het |
| Or5d38 |
A |
T |
2: 87,954,981 (GRCm39) |
M116K |
possibly damaging |
Het |
| Oxsm |
A |
T |
14: 16,242,045 (GRCm38) |
S241R |
probably damaging |
Het |
| Pde1a |
G |
T |
2: 79,736,372 (GRCm39) |
S87R |
probably damaging |
Het |
| Plagl2 |
A |
T |
2: 153,074,114 (GRCm39) |
C262* |
probably null |
Het |
| Plcg2 |
A |
G |
8: 118,361,140 (GRCm39) |
K1233R |
probably benign |
Het |
| Pon3 |
A |
T |
6: 5,256,177 (GRCm39) |
I17K |
possibly damaging |
Het |
| Ppfia1 |
A |
T |
7: 144,045,229 (GRCm39) |
M951K |
probably benign |
Het |
| Pramel12 |
A |
G |
4: 143,145,874 (GRCm39) |
R448G |
probably damaging |
Het |
| Prpf31 |
A |
G |
7: 3,642,824 (GRCm39) |
K438E |
probably benign |
Het |
| Pum3 |
C |
A |
19: 27,396,248 (GRCm39) |
V328F |
probably damaging |
Het |
| Ralgapa1 |
T |
C |
12: 55,723,495 (GRCm39) |
E1677G |
probably benign |
Het |
| Rpf2 |
A |
G |
10: 40,103,627 (GRCm39) |
V96A |
possibly damaging |
Het |
| Rsrc2 |
C |
T |
5: 123,869,150 (GRCm39) |
A98T |
probably damaging |
Het |
| Saraf |
G |
A |
8: 34,628,412 (GRCm39) |
R86Q |
probably damaging |
Het |
| Scara5 |
T |
A |
14: 65,977,788 (GRCm39) |
D349E |
possibly damaging |
Het |
| Slc30a1 |
T |
C |
1: 191,641,734 (GRCm39) |
V460A |
possibly damaging |
Het |
| Tdrd7 |
G |
T |
4: 46,020,877 (GRCm39) |
V768L |
possibly damaging |
Het |
| Tshz2 |
T |
C |
2: 169,725,718 (GRCm39) |
S105P |
probably benign |
Het |
| Ufsp2 |
A |
G |
8: 46,445,258 (GRCm39) |
I362M |
probably damaging |
Het |
| Ugt1a7c |
T |
A |
1: 88,023,159 (GRCm39) |
I106K |
probably benign |
Het |
| Zdhhc5 |
A |
G |
2: 84,520,810 (GRCm39) |
Y456H |
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 |
|
|
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 |
|
|
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'- CCAACTTTGCCTTGAGGACC -3'
(R):5'- TTCCCAGGTCAAGATGGTCTG -3'
Sequencing Primer
(F):5'- TTGAGGACCAGCGTCACCAG -3'
(R):5'- TCAAGATGGTCTGGCAGGTCC -3'
|
| Posted On |
2016-10-06 |
Incidental Mutation