Incidental Mutation 'R6549:Col25a1'
| ID |
521429 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col25a1
|
| Ensembl Gene |
ENSMUSG00000058897 |
| Gene Name |
collagen, type XXV, alpha 1 |
| Synonyms |
2700062B08Rik |
| MMRRC Submission |
044674-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.136)
|
| Stock # |
R6549 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
129973992-130393533 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 129976444 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 110
(T110A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000138875
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000080335]
[ENSMUST00000106353]
[ENSMUST00000183368]
|
| AlphaFold |
Q99MQ5 |
| Predicted Effect |
unknown
Transcript: ENSMUST00000080335
AA Change: T110A
|
| SMART Domains |
Protein: ENSMUSP00000079210
Gene: ENSMUSG00000058897
AA Change: T110A
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
35 |
47 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
119 |
165 |
7e-9 |
PFAM |
|
low complexity region
|
188 |
246 |
N/A |
INTRINSIC |
|
low complexity region
|
275 |
288 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
311 |
374 |
5.4e-11 |
PFAM |
|
Pfam:Collagen
|
368 |
427 |
2e-9 |
PFAM |
|
Pfam:Collagen
|
447 |
504 |
1.6e-10 |
PFAM |
|
Pfam:Collagen
|
494 |
561 |
3.3e-8 |
PFAM |
|
Pfam:Collagen
|
586 |
660 |
4.3e-11 |
PFAM |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000106353
AA Change: T110A
|
| SMART Domains |
Protein: ENSMUSP00000101960
Gene: ENSMUSG00000058897
AA Change: T110A
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
35 |
47 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
119 |
174 |
1.7e-11 |
PFAM |
|
Pfam:Collagen
|
183 |
244 |
6.2e-12 |
PFAM |
|
Pfam:Collagen
|
233 |
297 |
7.5e-11 |
PFAM |
|
Pfam:Collagen
|
294 |
345 |
1.8e-9 |
PFAM |
|
Pfam:Collagen
|
343 |
399 |
1.1e-10 |
PFAM |
|
Pfam:Collagen
|
419 |
475 |
1.9e-10 |
PFAM |
|
low complexity region
|
490 |
525 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
555 |
622 |
6e-12 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143830
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000183368
AA Change: T110A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897
AA Change: T110A
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
35 |
47 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
119 |
165 |
6.8e-9 |
PFAM |
|
low complexity region
|
188 |
246 |
N/A |
INTRINSIC |
|
internal_repeat_2
|
249 |
294 |
2.8e-5 |
PROSPERO |
|
internal_repeat_1
|
294 |
308 |
4.06e-8 |
PROSPERO |
|
Pfam:Collagen
|
309 |
372 |
2.1e-11 |
PFAM |
|
Pfam:Collagen
|
371 |
427 |
3.7e-10 |
PFAM |
|
Pfam:Collagen
|
447 |
496 |
7.7e-10 |
PFAM |
|
low complexity region
|
497 |
506 |
N/A |
INTRINSIC |
|
low complexity region
|
514 |
527 |
N/A |
INTRINSIC |
|
low complexity region
|
556 |
571 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000197950
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.3%
- 20x: 97.7%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a brain-specific membrane associated collagen. A product of proteolytic processing of the encoded protein, CLAC (collagenous Alzheimer amyloid plaque component), binds to amyloid beta-peptides found in Alzheimer amyloid plaques but CLAC inhibits rather than facilitates amyloid fibril elongation (PMID: 16300410). A study of over-expression of this collagen in mice, however, found changes in pathology and behavior suggesting that the encoded protein may promote amyloid plaque formation (PMID: 19548013). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit neonatal lethality, cyanosis and abnormal body curvature with apoptosis of phrenic nerve motor neurons and failure of diaphragm innervation. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 25 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Atm |
T |
C |
9: 53,404,477 (GRCm39) |
D1288G |
probably benign |
Het |
| Atxn7 |
T |
C |
14: 14,013,087 (GRCm38) |
S2P |
probably damaging |
Het |
| C1rl |
T |
A |
6: 124,485,487 (GRCm39) |
I286N |
probably benign |
Het |
| Ccdc54 |
T |
C |
16: 50,410,388 (GRCm39) |
R293G |
possibly damaging |
Het |
| Cndp1 |
A |
T |
18: 84,654,309 (GRCm39) |
I85K |
probably benign |
Het |
| Defb8 |
G |
T |
8: 19,497,560 (GRCm39) |
P17Q |
probably damaging |
Het |
| Dnah1 |
A |
T |
14: 30,991,340 (GRCm39) |
L3146Q |
probably damaging |
Het |
| Espn |
A |
T |
4: 152,215,525 (GRCm39) |
M1K |
probably null |
Het |
| Gm9922 |
C |
A |
14: 101,966,893 (GRCm39) |
|
probably benign |
Het |
| Hycc2 |
T |
C |
1: 58,578,759 (GRCm39) |
I264V |
probably benign |
Het |
| Ldb3 |
A |
G |
14: 34,263,854 (GRCm39) |
M545T |
probably damaging |
Het |
| Or8k30 |
A |
T |
2: 86,339,726 (GRCm39) |
I308L |
probably benign |
Het |
| Piezo1 |
G |
A |
8: 123,227,002 (GRCm39) |
H420Y |
|
Het |
| Primpol |
A |
T |
8: 47,058,185 (GRCm39) |
L115I |
probably damaging |
Het |
| Pus10 |
G |
A |
11: 23,679,075 (GRCm39) |
|
probably null |
Het |
| Rictor |
C |
G |
15: 6,825,656 (GRCm39) |
A1689G |
probably damaging |
Het |
| Scn2a |
A |
G |
2: 65,595,018 (GRCm39) |
N1956D |
probably benign |
Het |
| Scn4a |
T |
C |
11: 106,234,791 (GRCm39) |
D384G |
probably damaging |
Het |
| Sell |
A |
G |
1: 163,893,198 (GRCm39) |
D138G |
probably damaging |
Het |
| Slc4a7 |
T |
A |
14: 14,748,564 (GRCm38) |
F327L |
probably damaging |
Het |
| Sox6 |
A |
G |
7: 115,085,927 (GRCm39) |
I680T |
possibly damaging |
Het |
| Synj1 |
A |
G |
16: 90,735,565 (GRCm39) |
S1463P |
probably benign |
Het |
| Vmn1r31 |
A |
T |
6: 58,449,648 (GRCm39) |
N72K |
possibly damaging |
Het |
| Vmn2r77 |
A |
G |
7: 86,450,065 (GRCm39) |
I104V |
probably benign |
Het |
| Zfp988 |
G |
A |
4: 147,416,310 (GRCm39) |
C248Y |
probably benign |
Het |
|
| Other mutations in Col25a1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00336:Col25a1
|
APN |
3 |
129,975,433 (GRCm39) |
splice site |
probably benign |
|
|
IGL00570:Col25a1
|
APN |
3 |
130,340,081 (GRCm39) |
splice site |
probably benign |
|
|
IGL01651:Col25a1
|
APN |
3 |
130,360,134 (GRCm39) |
missense |
probably benign |
0.06 |
|
IGL02033:Col25a1
|
APN |
3 |
130,182,597 (GRCm39) |
splice site |
probably benign |
|
|
IGL02117:Col25a1
|
APN |
3 |
130,313,422 (GRCm39) |
splice site |
probably benign |
|
|
IGL02290:Col25a1
|
APN |
3 |
130,313,460 (GRCm39) |
splice site |
probably benign |
|
|
IGL03135:Col25a1
|
APN |
3 |
130,323,332 (GRCm39) |
splice site |
probably benign |
|
|
R0526:Col25a1
|
UTSW |
3 |
130,270,043 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0602:Col25a1
|
UTSW |
3 |
130,369,063 (GRCm39) |
splice site |
probably null |
|
|
R0670:Col25a1
|
UTSW |
3 |
130,180,544 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R0830:Col25a1
|
UTSW |
3 |
130,378,375 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1220:Col25a1
|
UTSW |
3 |
130,182,574 (GRCm39) |
splice site |
probably benign |
|
|
R1623:Col25a1
|
UTSW |
3 |
130,343,699 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1818:Col25a1
|
UTSW |
3 |
130,379,386 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2142:Col25a1
|
UTSW |
3 |
130,363,965 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2190:Col25a1
|
UTSW |
3 |
130,378,364 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2901:Col25a1
|
UTSW |
3 |
130,340,040 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2902:Col25a1
|
UTSW |
3 |
130,340,040 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3703:Col25a1
|
UTSW |
3 |
130,343,682 (GRCm39) |
splice site |
probably null |
|
|
R3818:Col25a1
|
UTSW |
3 |
130,343,720 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R4726:Col25a1
|
UTSW |
3 |
130,313,430 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R4775:Col25a1
|
UTSW |
3 |
129,976,468 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
R5036:Col25a1
|
UTSW |
3 |
130,376,978 (GRCm39) |
splice site |
probably null |
|
|
R5110:Col25a1
|
UTSW |
3 |
130,378,374 (GRCm39) |
makesense |
probably null |
|
|
R5501:Col25a1
|
UTSW |
3 |
130,389,312 (GRCm39) |
missense |
probably benign |
0.07 |
|
R5686:Col25a1
|
UTSW |
3 |
130,357,803 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5698:Col25a1
|
UTSW |
3 |
130,272,632 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R6131:Col25a1
|
UTSW |
3 |
130,329,114 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6142:Col25a1
|
UTSW |
3 |
130,376,978 (GRCm39) |
splice site |
probably benign |
|
|
R6624:Col25a1
|
UTSW |
3 |
130,360,100 (GRCm39) |
splice site |
probably null |
|
|
R6898:Col25a1
|
UTSW |
3 |
130,378,377 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7030:Col25a1
|
UTSW |
3 |
130,272,671 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7114:Col25a1
|
UTSW |
3 |
130,389,324 (GRCm39) |
missense |
probably benign |
0.06 |
|
R7172:Col25a1
|
UTSW |
3 |
130,363,981 (GRCm39) |
nonsense |
probably null |
|
|
R7179:Col25a1
|
UTSW |
3 |
130,323,768 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7340:Col25a1
|
UTSW |
3 |
130,340,006 (GRCm39) |
splice site |
probably null |
|
|
R7488:Col25a1
|
UTSW |
3 |
130,378,350 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7699:Col25a1
|
UTSW |
3 |
130,316,128 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7976:Col25a1
|
UTSW |
3 |
130,290,075 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8129:Col25a1
|
UTSW |
3 |
130,290,050 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8199:Col25a1
|
UTSW |
3 |
130,345,628 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8524:Col25a1
|
UTSW |
3 |
130,342,873 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8809:Col25a1
|
UTSW |
3 |
130,354,466 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R8973:Col25a1
|
UTSW |
3 |
130,269,275 (GRCm39) |
missense |
unknown |
|
|
R9059:Col25a1
|
UTSW |
3 |
130,268,499 (GRCm39) |
missense |
unknown |
|
|
X0028:Col25a1
|
UTSW |
3 |
130,370,967 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
Z1176:Col25a1
|
UTSW |
3 |
129,976,444 (GRCm39) |
frame shift |
probably null |
|
|
Z1177:Col25a1
|
UTSW |
3 |
130,316,110 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCCTGCTACCATGTCAGTGG -3'
(R):5'- TTTTATTAAAGCAGGTTGGGCC -3'
Sequencing Primer
(F):5'- CTGTTACTTTTTGACAAGAGTCCAAG -3'
(R):5'- GGGCCTGCAGTCTTTCTTCAC -3'
|
| Posted On |
2018-06-06 |
Incidental Mutation