Incidental Mutation 'R0691:Col10a1'
| ID |
63967 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col10a1
|
| Ensembl Gene |
ENSMUSG00000039462 |
| Gene Name |
collagen, type X, alpha 1 |
| Synonyms |
Col10, Col10a-1 |
| MMRRC Submission |
038876-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.121)
|
| Stock # |
R0691 (G1)
|
| Quality Score |
105 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
34265977-34273081 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 34271692 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 555
(T555A)
|
| 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 |
possibly damaging
Transcript: ENSMUST00000105511
AA Change: T555A
PolyPhen 2
Score 0.945 (Sensitivity: 0.80; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000101150
Gene: ENSMUSG00000039462
AA Change: T555A
| 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 |
0.1218 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.8%
- 10x: 97.5%
- 20x: 95.4%
|
| Validation Efficiency |
97% (58/60) |
| 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 |
|---|
| Abcc9 |
T |
C |
6: 142,584,979 (GRCm39) |
D865G |
possibly damaging |
Het |
| Acy1 |
A |
T |
9: 106,313,070 (GRCm39) |
|
probably null |
Het |
| Adcy4 |
A |
T |
14: 56,010,104 (GRCm39) |
|
probably benign |
Het |
| Anpep |
T |
G |
7: 79,489,047 (GRCm39) |
D347A |
probably damaging |
Het |
| Arhgap28 |
C |
T |
17: 68,203,159 (GRCm39) |
|
probably null |
Het |
| Ccdc32 |
A |
G |
2: 118,857,610 (GRCm39) |
|
probably benign |
Het |
| Cdc42bpa |
A |
G |
1: 179,972,400 (GRCm39) |
T1401A |
possibly damaging |
Het |
| Celsr2 |
A |
G |
3: 108,319,939 (GRCm39) |
Y958H |
probably damaging |
Het |
| Cenpe |
A |
G |
3: 134,923,066 (GRCm39) |
E137G |
probably damaging |
Het |
| Chd8 |
T |
C |
14: 52,450,890 (GRCm39) |
D1399G |
probably damaging |
Het |
| Cntn3 |
T |
C |
6: 102,145,908 (GRCm39) |
T978A |
possibly damaging |
Het |
| Crybg3 |
A |
C |
16: 59,385,574 (GRCm39) |
|
probably null |
Het |
| Cts7 |
A |
G |
13: 61,503,548 (GRCm39) |
F139L |
probably damaging |
Het |
| Dera |
T |
C |
6: 137,773,745 (GRCm39) |
|
probably benign |
Het |
| Dgka |
A |
G |
10: 128,559,129 (GRCm39) |
|
probably benign |
Het |
| Dhrs7 |
T |
A |
12: 72,699,125 (GRCm39) |
I286F |
probably damaging |
Het |
| Dtwd2 |
A |
G |
18: 49,861,424 (GRCm39) |
|
probably benign |
Het |
| Fermt1 |
A |
G |
2: 132,748,653 (GRCm39) |
S657P |
probably damaging |
Het |
| Fhip2b |
T |
C |
14: 70,825,727 (GRCm39) |
D351G |
probably damaging |
Het |
| Flnb |
T |
C |
14: 7,890,810 (GRCm38) |
V564A |
probably benign |
Het |
| Garnl3 |
A |
G |
2: 32,975,919 (GRCm39) |
F16L |
probably damaging |
Het |
| Gck |
T |
C |
11: 5,856,691 (GRCm39) |
R191G |
probably damaging |
Het |
| Gucy1b1 |
A |
T |
3: 81,952,941 (GRCm39) |
|
probably benign |
Het |
| Ifna2 |
A |
C |
4: 88,601,895 (GRCm39) |
L41R |
probably damaging |
Het |
| Krt33a |
T |
G |
11: 99,903,541 (GRCm39) |
E197A |
probably damaging |
Het |
| Lce1e |
G |
A |
3: 92,615,063 (GRCm39) |
R95C |
unknown |
Het |
| Lct |
G |
T |
1: 128,235,971 (GRCm39) |
S345R |
probably benign |
Het |
| Lrp2 |
A |
T |
2: 69,281,724 (GRCm39) |
N3882K |
probably benign |
Het |
| Mcc |
G |
T |
18: 44,578,927 (GRCm39) |
T652K |
possibly damaging |
Het |
| Mier1 |
A |
G |
4: 102,996,699 (GRCm39) |
S109G |
probably benign |
Het |
| Nfat5 |
A |
G |
8: 108,082,237 (GRCm39) |
N469S |
probably damaging |
Het |
| Or1e23 |
C |
A |
11: 73,407,670 (GRCm39) |
M118I |
possibly damaging |
Het |
| Or6c214 |
G |
A |
10: 129,591,271 (GRCm39) |
T16I |
probably damaging |
Het |
| Piwil1 |
G |
T |
5: 128,820,371 (GRCm39) |
R256M |
probably null |
Het |
| Rgma |
T |
C |
7: 73,059,160 (GRCm39) |
V88A |
probably damaging |
Het |
| Sdk2 |
T |
C |
11: 113,685,746 (GRCm39) |
|
probably null |
Het |
| Sec22b |
A |
G |
3: 97,819,990 (GRCm39) |
E94G |
probably damaging |
Het |
| Snrnp70 |
T |
C |
7: 45,036,669 (GRCm39) |
R131G |
possibly damaging |
Het |
| Spata31d1a |
A |
G |
13: 59,848,199 (GRCm39) |
S1310P |
possibly damaging |
Het |
| Spint1 |
A |
G |
2: 119,076,948 (GRCm39) |
E344G |
probably damaging |
Het |
| Srrm1 |
G |
A |
4: 135,052,302 (GRCm39) |
Q141* |
probably null |
Het |
| Tecta |
A |
T |
9: 42,295,637 (GRCm39) |
L286Q |
probably damaging |
Het |
| Tep1 |
T |
A |
14: 51,104,301 (GRCm39) |
K198* |
probably null |
Het |
| Tk2 |
A |
G |
8: 104,957,824 (GRCm39) |
V174A |
probably benign |
Het |
| Txndc5 |
T |
C |
13: 38,691,872 (GRCm39) |
K165E |
probably damaging |
Het |
| Ubr4 |
G |
A |
4: 139,151,217 (GRCm39) |
R1884Q |
probably damaging |
Het |
| Vmn2r61 |
T |
C |
7: 41,949,844 (GRCm39) |
Y755H |
probably damaging |
Het |
| Xrn1 |
T |
A |
9: 95,855,592 (GRCm39) |
H296Q |
probably damaging |
Het |
| Zar1l |
A |
T |
5: 150,436,407 (GRCm39) |
V223D |
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 |
|
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 |
|
R4208:Col10a1
|
UTSW |
10 |
34,271,539 (GRCm39) |
missense |
probably damaging |
0.99 |
|
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'- GCATAGCAACTAAGGGCCTCAATGG -3'
(R):5'- ATTGCACTCCCTGAAGCCTGATCC -3'
Sequencing Primer
(F):5'- AGGCCCTCCTGGTCCAAG -3'
(R):5'- CTGAAGCCTGATCCAGGTAG -3'
|
| Posted On |
2013-07-30 |
Incidental Mutation