Incidental Mutation 'R6142:Col25a1'
| ID |
501856 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col25a1
|
| Ensembl Gene |
ENSMUSG00000058897 |
| Gene Name |
collagen, type XXV, alpha 1 |
| Synonyms |
2700062B08Rik |
| MMRRC Submission |
044289-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.136)
|
| Stock # |
R6142 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
129973992-130393533 bp(+) (GRCm39) |
| Type of Mutation |
splice site |
| DNA Base Change (assembly) |
T to A
at 130376978 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000138875
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000080335]
[ENSMUST00000106353]
[ENSMUST00000183368]
|
| AlphaFold |
Q99MQ5 |
| Predicted Effect |
probably benign
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 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 |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.9%
- 20x: 94.2%
|
| Validation Efficiency |
100% (48/48) |
| 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: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adcy6 |
T |
C |
15: 98,496,303 (GRCm39) |
M579V |
probably benign |
Het |
| Agtr1b |
T |
C |
3: 20,370,558 (GRCm39) |
D16G |
probably benign |
Het |
| Akap12 |
C |
A |
10: 4,263,740 (GRCm39) |
|
probably null |
Het |
| Alpk2 |
T |
C |
18: 65,438,456 (GRCm39) |
E979G |
possibly damaging |
Het |
| Arfgap3 |
T |
C |
15: 83,234,328 (GRCm39) |
D8G |
probably damaging |
Het |
| AW551984 |
G |
T |
9: 39,508,410 (GRCm39) |
L369I |
probably benign |
Het |
| Bmp8b |
A |
T |
4: 123,009,043 (GRCm39) |
H207L |
probably benign |
Het |
| Cc2d2a |
G |
T |
5: 43,860,540 (GRCm39) |
V490F |
probably damaging |
Het |
| Cnot6l |
C |
T |
5: 96,230,837 (GRCm39) |
V377I |
probably benign |
Het |
| Crocc2 |
C |
G |
1: 93,118,201 (GRCm39) |
Q375E |
possibly damaging |
Het |
| Ganc |
T |
C |
2: 120,261,218 (GRCm39) |
|
probably null |
Het |
| Gm28168 |
C |
A |
1: 117,875,678 (GRCm39) |
D102E |
probably benign |
Het |
| Gm8212 |
T |
C |
14: 44,438,684 (GRCm39) |
|
probably null |
Het |
| Gria2 |
T |
C |
3: 80,709,024 (GRCm39) |
T53A |
probably benign |
Het |
| Hipk4 |
G |
A |
7: 27,228,590 (GRCm39) |
V347M |
probably damaging |
Het |
| Hmgxb3 |
T |
C |
18: 61,269,309 (GRCm39) |
E991G |
probably benign |
Het |
| Hyal1 |
G |
A |
9: 107,456,573 (GRCm39) |
R420H |
probably benign |
Het |
| Il5 |
G |
A |
11: 53,611,805 (GRCm39) |
|
probably null |
Het |
| Kcnh7 |
T |
C |
2: 62,569,704 (GRCm39) |
I731V |
possibly damaging |
Het |
| Lamb2 |
A |
T |
9: 108,362,817 (GRCm39) |
K759* |
probably null |
Het |
| Lnpep |
A |
G |
17: 17,786,943 (GRCm39) |
|
probably null |
Het |
| Lrch1 |
T |
C |
14: 75,184,940 (GRCm39) |
E54G |
probably damaging |
Het |
| Msl3l2 |
A |
G |
10: 55,991,461 (GRCm39) |
D62G |
possibly damaging |
Het |
| Mslnl |
T |
C |
17: 25,963,531 (GRCm39) |
L339P |
probably damaging |
Het |
| Nfe2l2 |
T |
C |
2: 75,509,761 (GRCm39) |
I20V |
probably damaging |
Het |
| Pgm5 |
A |
C |
19: 24,801,772 (GRCm39) |
I152S |
probably damaging |
Het |
| Plcg2 |
C |
A |
8: 118,312,010 (GRCm39) |
T434K |
probably benign |
Het |
| Prrc2c |
T |
C |
1: 162,537,956 (GRCm39) |
E558G |
unknown |
Het |
| Ranbp3 |
T |
C |
17: 56,993,018 (GRCm39) |
V12A |
probably benign |
Het |
| Rgsl1 |
A |
G |
1: 153,687,984 (GRCm39) |
V635A |
probably benign |
Het |
| Rpap2 |
T |
C |
5: 107,746,164 (GRCm39) |
V14A |
probably benign |
Het |
| Rxrg |
G |
T |
1: 167,460,191 (GRCm39) |
A341S |
possibly damaging |
Het |
| Sbf2 |
A |
G |
7: 109,948,182 (GRCm39) |
S1177P |
probably damaging |
Het |
| Sema6a |
T |
C |
18: 47,414,266 (GRCm39) |
T498A |
probably benign |
Het |
| Slc13a4 |
G |
A |
6: 35,278,718 (GRCm39) |
A57V |
probably damaging |
Het |
| Slc6a3 |
A |
T |
13: 73,692,902 (GRCm39) |
D174V |
probably benign |
Het |
| Spart |
T |
G |
3: 55,024,669 (GRCm39) |
V88G |
probably damaging |
Het |
| Tanc1 |
A |
T |
2: 59,663,566 (GRCm39) |
R1108* |
probably null |
Het |
| Tas2r140 |
C |
T |
6: 133,032,698 (GRCm39) |
G20E |
probably damaging |
Het |
| Tdrd6 |
A |
G |
17: 43,940,373 (GRCm39) |
V225A |
probably benign |
Het |
| Tmem168 |
C |
A |
6: 13,591,368 (GRCm39) |
A99S |
probably benign |
Het |
| Tnk2 |
T |
A |
16: 32,488,917 (GRCm39) |
D252E |
probably damaging |
Het |
| Tpsg1 |
A |
T |
17: 25,591,460 (GRCm39) |
H20L |
probably benign |
Het |
| Tram1l1 |
T |
C |
3: 124,115,092 (GRCm39) |
F84S |
probably damaging |
Het |
| Vmn2r12 |
T |
A |
5: 109,240,763 (GRCm39) |
I117L |
probably benign |
Het |
| Zfp148 |
T |
C |
16: 33,315,829 (GRCm39) |
L219S |
possibly damaging |
Het |
| Zfp40 |
C |
A |
17: 23,395,311 (GRCm39) |
E425D |
probably benign |
Het |
| Zfp773 |
T |
C |
7: 7,135,481 (GRCm39) |
T372A |
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 |
|
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'- ATTTCAGCAGTCATCTGGCAG -3'
(R):5'- ATTTGAGGCCGAGTATGATCTG -3'
Sequencing Primer
(F):5'- CTTCGTCACTACAGTCTTGAAGGAG -3'
(R):5'- CCGAGTATGATCTGTCTGTAGCAC -3'
|
| Posted On |
2017-12-04 |
Incidental Mutation