Incidental Mutation 'R5036:Col25a1'
ID |
389530 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col25a1
|
Ensembl Gene |
ENSMUSG00000058897 |
Gene Name |
collagen, type XXV, alpha 1 |
Synonyms |
2700062B08Rik |
MMRRC Submission |
042627-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.136)
|
Stock # |
R5036 (G1)
|
Quality Score |
124 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
129973992-130393533 bp(+) (GRCm39) |
Type of Mutation |
splice site (6 bp from exon) |
DNA Base Change (assembly) |
T to C
at 130376978 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Ref Sequence |
ENSEMBL: ENSMUSP00000101960
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000080335]
[ENSMUST00000106353]
[ENSMUST00000106353]
[ENSMUST00000183368]
|
AlphaFold |
Q99MQ5 |
Predicted Effect |
probably null
Transcript: ENSMUST00000080335
|
SMART Domains |
Protein: ENSMUSP00000079210 Gene: ENSMUSG00000058897
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 null
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 null
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 |
|
Meta Mutation Damage Score |
0.9755 |
Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.2%
- 10x: 95.7%
- 20x: 90.1%
|
Validation Efficiency |
100% (44/44) |
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: 35 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
2610021A01Rik |
G |
A |
7: 41,275,578 (GRCm39) |
G427D |
possibly damaging |
Het |
Agbl5 |
G |
A |
5: 31,060,403 (GRCm39) |
R141Q |
probably damaging |
Het |
C4b |
T |
A |
17: 34,959,419 (GRCm39) |
|
probably null |
Het |
Cabyr |
A |
T |
18: 12,884,303 (GRCm39) |
E263D |
probably damaging |
Het |
Car1 |
A |
T |
3: 14,841,299 (GRCm39) |
D45E |
possibly damaging |
Het |
Dnah6 |
G |
T |
6: 73,021,674 (GRCm39) |
S3549R |
probably benign |
Het |
Dync1h1 |
A |
T |
12: 110,596,969 (GRCm39) |
I1639F |
probably damaging |
Het |
Fhad1 |
A |
T |
4: 141,648,052 (GRCm39) |
D271E |
probably benign |
Het |
Gle1 |
T |
C |
2: 29,826,223 (GRCm39) |
S101P |
probably benign |
Het |
Gm4781 |
C |
A |
10: 100,232,851 (GRCm39) |
|
noncoding transcript |
Het |
Gpatch3 |
A |
G |
4: 133,305,461 (GRCm39) |
Y232C |
probably damaging |
Het |
Gtf2ird2 |
A |
G |
5: 134,246,349 (GRCm39) |
N869S |
probably damaging |
Het |
Ifi204 |
G |
A |
1: 173,580,311 (GRCm39) |
P400S |
possibly damaging |
Het |
Ighv2-2 |
T |
C |
12: 113,552,092 (GRCm39) |
T49A |
possibly damaging |
Het |
Itsn1 |
T |
A |
16: 91,579,123 (GRCm39) |
|
probably benign |
Het |
Mib2 |
A |
T |
4: 155,740,745 (GRCm39) |
N626K |
probably damaging |
Het |
Nf1 |
C |
A |
11: 79,337,690 (GRCm39) |
Q1098K |
probably damaging |
Het |
Odc1 |
C |
A |
12: 17,598,020 (GRCm39) |
Q116K |
probably damaging |
Het |
Otof |
C |
T |
5: 30,541,783 (GRCm39) |
E761K |
possibly damaging |
Het |
Palld |
A |
T |
8: 62,003,196 (GRCm39) |
V301D |
probably damaging |
Het |
Pask |
A |
T |
1: 93,249,801 (GRCm39) |
L533* |
probably null |
Het |
Plekhh2 |
T |
C |
17: 84,879,189 (GRCm39) |
S638P |
probably damaging |
Het |
Scaf8 |
T |
A |
17: 3,214,537 (GRCm39) |
|
probably benign |
Het |
Sdccag8 |
G |
T |
1: 176,839,541 (GRCm39) |
R695L |
probably damaging |
Het |
Serpina1c |
A |
G |
12: 103,865,085 (GRCm39) |
I187T |
probably damaging |
Het |
Slitrk5 |
G |
T |
14: 111,918,316 (GRCm39) |
G647W |
possibly damaging |
Het |
Sycp1 |
T |
A |
3: 102,727,916 (GRCm39) |
K899M |
probably damaging |
Het |
Taok1 |
G |
A |
11: 77,440,157 (GRCm39) |
R617C |
probably benign |
Het |
Tbc1d32 |
A |
C |
10: 56,071,500 (GRCm39) |
Y341* |
probably null |
Het |
Tenm4 |
A |
G |
7: 96,343,997 (GRCm39) |
N267D |
probably damaging |
Het |
Tenm4 |
T |
C |
7: 96,501,768 (GRCm39) |
V1287A |
probably damaging |
Het |
Tsga10 |
A |
T |
1: 37,823,049 (GRCm39) |
V488E |
possibly damaging |
Het |
Ttc39c |
G |
T |
18: 12,820,138 (GRCm39) |
|
probably null |
Het |
Uck1 |
A |
T |
2: 32,148,478 (GRCm39) |
|
probably benign |
Het |
Vmn2r98 |
A |
G |
17: 19,286,419 (GRCm39) |
I306V |
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 |
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'- TTTCAGCAGTCATCTGGCAGC -3'
(R):5'- ATTTGAGGCCGAGTATGATCTG -3'
Sequencing Primer
(F):5'- CTTCGTCACTACAGTCTTGAAGGAG -3'
(R):5'- CCGAGTATGATCTGTCTGTAGCAC -3'
|
Posted On |
2016-06-06 |