Incidental Mutation 'R4208:Col10a1'
| ID |
319033 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col10a1
|
| Ensembl Gene |
ENSMUSG00000039462 |
| Gene Name |
collagen, type X, alpha 1 |
| Synonyms |
Col10, Col10a-1 |
| MMRRC Submission |
041037-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.121)
|
| Stock # |
R4208 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
34265977-34273081 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 34271539 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Proline to Serine
at position 504
(P504S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000101150
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000047885]
[ENSMUST00000099973]
[ENSMUST00000105511]
[ENSMUST00000105512]
[ENSMUST00000213269]
|
| AlphaFold |
Q05306 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000047885
|
| SMART Domains |
Protein: ENSMUSP00000047126
Gene: ENSMUSG00000039480
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:5_nucleotid
|
1 |
382 |
2.6e-58 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000099973
|
| SMART Domains |
Protein: ENSMUSP00000097553
Gene: ENSMUSG00000039480
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:5_nucleotid
|
1 |
189 |
8.8e-25 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000105511
AA Change: P504S
PolyPhen 2
Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000101150
Gene: ENSMUSG00000039462
AA Change: P504S
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
low complexity region
|
60 |
101 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
103 |
155 |
1.4e-9 |
PFAM |
|
Pfam:Collagen
|
153 |
218 |
1.4e-8 |
PFAM |
|
Pfam:Collagen
|
193 |
250 |
2.6e-9 |
PFAM |
|
Pfam:Collagen
|
206 |
264 |
3.8e-8 |
PFAM |
|
low complexity region
|
282 |
323 |
N/A |
INTRINSIC |
|
internal_repeat_2
|
329 |
361 |
2.25e-6 |
PROSPERO |
|
internal_repeat_1
|
331 |
365 |
5.9e-14 |
PROSPERO |
|
low complexity region
|
368 |
383 |
N/A |
INTRINSIC |
|
low complexity region
|
391 |
410 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
413 |
483 |
9.3e-10 |
PFAM |
|
low complexity region
|
487 |
517 |
N/A |
INTRINSIC |
|
C1Q
|
545 |
680 |
2.85e-79 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000105512
|
| SMART Domains |
Protein: ENSMUSP00000101151
Gene: ENSMUSG00000039480
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:5_nucleotid
|
1 |
372 |
8.7e-54 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130290
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000213269
|
| Meta Mutation Damage Score |
0.3218 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 95.1%
|
| Validation Efficiency |
100% (57/57) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the alpha chain of type X collagen, a short chain collagen expressed by hypertrophic chondrocytes during endochondral ossification. Unlike type VIII collagen, the other short chain collagen, type X collagen is a homotrimer. Mutations in this gene are associated with Schmid type metaphyseal chondrodysplasia (SMCD) and Japanese type spondylometaphyseal dysplasia (SMD). [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations may exhibit abnormal trabecular bone, thinner growth plate resting zone and articular cartilage, and altered bone content. Mice homozygous for another knock-out allele exhibit altered B and T cell populations and TH1/TH2responses. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 49 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A1cf |
T |
C |
19: 31,910,060 (GRCm39) |
L284P |
probably benign |
Het |
| Abca8b |
G |
A |
11: 109,872,551 (GRCm39) |
Q17* |
probably null |
Het |
| Abcc6 |
A |
C |
7: 45,635,987 (GRCm39) |
L1020R |
probably damaging |
Het |
| Ace2 |
A |
G |
X: 162,952,581 (GRCm39) |
I110V |
probably benign |
Het |
| Adamts12 |
A |
G |
15: 11,071,840 (GRCm39) |
H128R |
probably benign |
Het |
| Aoc1l2 |
A |
T |
6: 48,908,581 (GRCm39) |
D527V |
probably damaging |
Het |
| Apol9a |
G |
C |
15: 77,288,596 (GRCm39) |
T257S |
probably benign |
Het |
| B4galnt3 |
A |
G |
6: 120,192,063 (GRCm39) |
S557P |
probably damaging |
Het |
| C3 |
C |
T |
17: 57,512,303 (GRCm39) |
D1542N |
possibly damaging |
Het |
| Casp12 |
T |
C |
9: 5,346,629 (GRCm39) |
L52P |
probably damaging |
Het |
| Cep126 |
C |
T |
9: 8,100,822 (GRCm39) |
E571K |
probably damaging |
Het |
| Cfhr1 |
A |
G |
1: 139,475,616 (GRCm39) |
|
probably benign |
Het |
| Cmah |
A |
G |
13: 24,601,410 (GRCm39) |
|
probably null |
Het |
| Ctnna3 |
T |
A |
10: 64,795,557 (GRCm39) |
D758E |
probably benign |
Het |
| Cyp2c65 |
T |
C |
19: 39,079,099 (GRCm39) |
S393P |
probably damaging |
Het |
| Dclk2 |
A |
G |
3: 86,738,129 (GRCm39) |
|
probably null |
Het |
| Dis3 |
T |
G |
14: 99,332,752 (GRCm39) |
I227L |
probably benign |
Het |
| Efhc2 |
T |
C |
X: 17,096,789 (GRCm39) |
N186S |
possibly damaging |
Het |
| F13b |
G |
T |
1: 139,444,079 (GRCm39) |
W471L |
probably damaging |
Het |
| Fam181a |
A |
G |
12: 103,282,173 (GRCm39) |
D26G |
probably damaging |
Het |
| Gabpb2 |
A |
G |
3: 95,111,245 (GRCm39) |
|
probably benign |
Het |
| Gm7293 |
A |
G |
9: 51,534,879 (GRCm39) |
|
noncoding transcript |
Het |
| H3f3a |
C |
T |
1: 180,630,703 (GRCm39) |
R117H |
probably benign |
Het |
| Ino80b |
G |
C |
6: 83,099,314 (GRCm39) |
P178R |
probably damaging |
Het |
| Kif3b |
G |
A |
2: 153,165,477 (GRCm39) |
R628Q |
probably damaging |
Het |
| Lars1 |
T |
C |
18: 42,362,768 (GRCm39) |
E557G |
probably benign |
Het |
| Ldlrad3 |
C |
T |
2: 101,783,507 (GRCm39) |
D240N |
probably damaging |
Het |
| Lingo2 |
T |
C |
4: 35,709,810 (GRCm39) |
I57V |
probably benign |
Het |
| Lsr |
A |
G |
7: 30,672,519 (GRCm39) |
I27T |
probably benign |
Het |
| Me2 |
T |
C |
18: 73,924,156 (GRCm39) |
K352R |
probably benign |
Het |
| Met |
T |
C |
6: 17,548,728 (GRCm39) |
V924A |
possibly damaging |
Het |
| Mpp3 |
T |
C |
11: 101,891,426 (GRCm39) |
T571A |
probably benign |
Het |
| Or4c1 |
A |
T |
2: 89,133,270 (GRCm39) |
I222N |
probably damaging |
Het |
| Or52n3 |
A |
G |
7: 104,530,810 (GRCm39) |
T299A |
probably damaging |
Het |
| Padi1 |
C |
A |
4: 140,544,538 (GRCm39) |
V552L |
possibly damaging |
Het |
| Pfkfb1 |
A |
T |
X: 149,405,184 (GRCm39) |
D208V |
possibly damaging |
Het |
| Rnase4 |
A |
G |
14: 51,342,462 (GRCm39) |
K62R |
probably benign |
Het |
| RP24-126A19.1 |
C |
A |
5: 146,832,606 (GRCm39) |
R123L |
noncoding transcript |
Het |
| Scn10a |
T |
A |
9: 119,445,842 (GRCm39) |
E1438V |
probably damaging |
Het |
| Sfmbt2 |
T |
A |
2: 10,547,793 (GRCm39) |
D458E |
probably damaging |
Het |
| Slitrk3 |
T |
A |
3: 72,958,490 (GRCm39) |
Y94F |
possibly damaging |
Het |
| Sstr2 |
A |
C |
11: 113,515,482 (GRCm39) |
T134P |
probably damaging |
Het |
| Steap4 |
A |
G |
5: 8,030,404 (GRCm39) |
Y420C |
probably damaging |
Het |
| Tamm41 |
AGGG |
AGG |
6: 114,989,320 (GRCm39) |
|
probably benign |
Het |
| Trav7-3 |
A |
G |
14: 53,681,203 (GRCm39) |
T82A |
probably benign |
Het |
| Trbv23 |
A |
T |
6: 41,193,022 (GRCm39) |
I6F |
probably benign |
Het |
| Vmn1r87 |
A |
G |
7: 12,866,185 (GRCm39) |
V34A |
probably benign |
Het |
| Zc3h7a |
C |
T |
16: 10,982,508 (GRCm39) |
E6K |
possibly damaging |
Het |
| Zfp606 |
G |
A |
7: 12,228,102 (GRCm39) |
C683Y |
probably damaging |
Het |
|
| Other mutations in Col10a1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL03005:Col10a1
|
APN |
10 |
34,271,734 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03028:Col10a1
|
APN |
10 |
34,271,012 (GRCm39) |
missense |
probably benign |
0.19 |
|
R0580:Col10a1
|
UTSW |
10 |
34,270,948 (GRCm39) |
missense |
probably benign |
0.31 |
|
R0691:Col10a1
|
UTSW |
10 |
34,271,692 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R1187:Col10a1
|
UTSW |
10 |
34,270,834 (GRCm39) |
missense |
probably benign |
0.13 |
|
R1597:Col10a1
|
UTSW |
10 |
34,271,074 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1724:Col10a1
|
UTSW |
10 |
34,271,714 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1826:Col10a1
|
UTSW |
10 |
34,270,645 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1834:Col10a1
|
UTSW |
10 |
34,271,011 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2156:Col10a1
|
UTSW |
10 |
34,271,696 (GRCm39) |
missense |
probably benign |
0.30 |
|
R3687:Col10a1
|
UTSW |
10 |
34,271,494 (GRCm39) |
missense |
probably benign |
0.12 |
|
R4929:Col10a1
|
UTSW |
10 |
34,271,120 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5411:Col10a1
|
UTSW |
10 |
34,270,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5433:Col10a1
|
UTSW |
10 |
34,266,735 (GRCm39) |
intron |
probably benign |
|
|
R5481:Col10a1
|
UTSW |
10 |
34,271,660 (GRCm39) |
missense |
probably benign |
0.09 |
|
R6036:Col10a1
|
UTSW |
10 |
34,271,278 (GRCm39) |
missense |
probably benign |
|
|
R6036:Col10a1
|
UTSW |
10 |
34,271,278 (GRCm39) |
missense |
probably benign |
|
|
R6208:Col10a1
|
UTSW |
10 |
34,270,582 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R6223:Col10a1
|
UTSW |
10 |
34,271,183 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7019:Col10a1
|
UTSW |
10 |
34,270,947 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R7642:Col10a1
|
UTSW |
10 |
34,271,638 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7784:Col10a1
|
UTSW |
10 |
34,270,214 (GRCm39) |
missense |
unknown |
|
|
R8072:Col10a1
|
UTSW |
10 |
34,266,663 (GRCm39) |
missense |
unknown |
|
|
R8711:Col10a1
|
UTSW |
10 |
34,270,824 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Col10a1
|
UTSW |
10 |
34,271,174 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGGAATACCAGGTACCAGGG -3'
(R):5'- TGCTGCTGCCTATTGTACAG -3'
Sequencing Primer
(F):5'- TACCAGGGGCCCCACTG -3'
(R):5'- GCACCTACTGCTGGGTAAG -3'
|
| Posted On |
2015-06-10 |
Incidental Mutation