Incidental Mutation 'R0830:Col25a1'
| ID |
77477 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col25a1
|
| Ensembl Gene |
ENSMUSG00000058897 |
| Gene Name |
collagen, type XXV, alpha 1 |
| Synonyms |
2700062B08Rik |
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.100)
|
| Stock # |
R0830 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
129973992-130393533 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 130378375 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glutamic Acid
at position 609
(D609E)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000079210
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000080335]
[ENSMUST00000106353]
[ENSMUST00000183368]
|
| AlphaFold |
Q99MQ5 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000080335
AA Change: D609E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000079210
Gene: ENSMUSG00000058897
AA Change: D609E
| 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 |
probably benign
Transcript: ENSMUST00000106353
|
| SMART Domains |
Protein: ENSMUSP00000101960
Gene: ENSMUSG00000058897
| 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 |
probably benign
Transcript: ENSMUST00000183368
|
| SMART Domains |
Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897
| 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 |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.4%
- 10x: 96.0%
- 20x: 90.6%
|
| 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: 41 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700056E22Rik |
C |
T |
1: 183,765,624 (GRCm39) |
R145H |
probably damaging |
Het |
| Adam26a |
C |
T |
8: 44,021,439 (GRCm39) |
V684I |
probably benign |
Het |
| Alk |
T |
C |
17: 72,910,195 (GRCm39) |
I170M |
probably benign |
Het |
| Apc2 |
T |
C |
10: 80,151,239 (GRCm39) |
Y2069H |
probably damaging |
Het |
| Aspm |
A |
G |
1: 139,401,992 (GRCm39) |
T1219A |
probably damaging |
Het |
| Bnip1 |
T |
C |
17: 27,008,679 (GRCm39) |
S94P |
probably benign |
Het |
| Cftr |
A |
G |
6: 18,270,224 (GRCm39) |
I805V |
probably benign |
Het |
| Cplane1 |
T |
A |
15: 8,276,669 (GRCm39) |
V2771E |
unknown |
Het |
| Cyp2g1 |
A |
G |
7: 26,514,216 (GRCm39) |
K274R |
probably benign |
Het |
| D5Ertd579e |
G |
A |
5: 36,771,101 (GRCm39) |
T1098I |
probably damaging |
Het |
| Ddx39a |
T |
A |
8: 84,446,452 (GRCm39) |
C74S |
possibly damaging |
Het |
| E2f3 |
C |
T |
13: 30,169,543 (GRCm39) |
A37T |
probably benign |
Het |
| Emilin2 |
A |
G |
17: 71,580,815 (GRCm39) |
M637T |
probably benign |
Het |
| Exosc7 |
T |
C |
9: 122,948,358 (GRCm39) |
L93P |
probably benign |
Het |
| F2 |
T |
C |
2: 91,460,545 (GRCm39) |
E316G |
probably benign |
Het |
| Fat4 |
A |
C |
3: 39,053,258 (GRCm39) |
Q4084P |
probably benign |
Het |
| Flywch1 |
T |
C |
17: 23,981,344 (GRCm39) |
K160E |
probably benign |
Het |
| Foxi2 |
A |
G |
7: 135,013,459 (GRCm39) |
T230A |
probably benign |
Het |
| Fthl17a |
A |
G |
X: 84,313,679 (GRCm39) |
N154S |
possibly damaging |
Het |
| Hykk |
G |
A |
9: 54,844,601 (GRCm39) |
R222Q |
probably damaging |
Het |
| Il18rap |
T |
A |
1: 40,582,150 (GRCm39) |
V357E |
probably damaging |
Het |
| Ing4 |
A |
G |
6: 125,020,923 (GRCm39) |
E15G |
probably damaging |
Het |
| Irak1 |
T |
C |
X: 73,060,189 (GRCm39) |
D679G |
probably damaging |
Het |
| Itga1 |
T |
C |
13: 115,143,568 (GRCm39) |
E321G |
probably benign |
Het |
| Nudt1 |
T |
A |
5: 140,321,076 (GRCm39) |
|
probably null |
Het |
| Nup58 |
A |
G |
14: 60,480,931 (GRCm39) |
F138S |
probably damaging |
Het |
| Or10al6 |
A |
T |
17: 38,082,804 (GRCm39) |
M87L |
probably damaging |
Het |
| Or2a5 |
G |
T |
6: 42,873,532 (GRCm39) |
W49L |
probably benign |
Het |
| Pllp |
T |
C |
8: 95,406,103 (GRCm39) |
Y60C |
probably damaging |
Het |
| Pnpla7 |
T |
C |
2: 24,887,267 (GRCm39) |
V37A |
probably damaging |
Het |
| Poglut3 |
T |
G |
9: 53,302,011 (GRCm39) |
L32R |
probably damaging |
Het |
| Psme4 |
A |
G |
11: 30,757,797 (GRCm39) |
H310R |
possibly damaging |
Het |
| Rasl10b |
G |
A |
11: 83,308,665 (GRCm39) |
|
probably null |
Het |
| Sash1 |
C |
T |
10: 8,605,673 (GRCm39) |
V906M |
probably benign |
Het |
| Scn1a |
A |
T |
2: 66,130,128 (GRCm39) |
I1212K |
probably damaging |
Het |
| Stbd1 |
A |
T |
5: 92,752,989 (GRCm39) |
S160C |
probably benign |
Het |
| Tex29 |
T |
C |
8: 11,904,157 (GRCm39) |
V99A |
probably benign |
Het |
| Tg |
A |
T |
15: 66,596,993 (GRCm39) |
N79I |
probably damaging |
Het |
| Tie1 |
T |
C |
4: 118,339,860 (GRCm39) |
D389G |
probably damaging |
Het |
| Vmn1r178 |
A |
G |
7: 23,593,452 (GRCm39) |
T167A |
possibly damaging |
Het |
| Xkr4 |
C |
T |
1: 3,740,968 (GRCm39) |
G202S |
possibly damaging |
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 |
|
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 |
|
|
R6549:Col25a1
|
UTSW |
3 |
129,976,444 (GRCm39) |
missense |
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'- GGCCTTTCCACATCTCCAGCATAG -3'
(R):5'- AGGTCATGCCGATGTTGAGTGTCC -3'
Sequencing Primer
(F):5'- TCCAGCATAGCCGTTTGAATAC -3'
(R):5'- GAAAGTACCACTATGCAATGTCAG -3'
|
| Posted On |
2013-10-16 |
Incidental Mutation