Incidental Mutation 'R3703:Col25a1'
| ID |
258599 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col25a1
|
| Ensembl Gene |
ENSMUSG00000058897 |
| Gene Name |
collagen, type XXV, alpha 1 |
| Synonyms |
2700062B08Rik |
| MMRRC Submission |
040696-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.100)
|
| Stock # |
R3703 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
129973992-130393533 bp(+) (GRCm39) |
| Type of Mutation |
splice site |
| DNA Base Change (assembly) |
A to G
at 130343682 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 |
noncoding transcript
Transcript: ENSMUST00000143830
|
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000196743
|
| Meta Mutation Damage Score |
0.9755 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.9%
- 20x: 93.7%
|
| Validation Efficiency |
100% (50/50) |
| 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: 47 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Arhgap10 |
C |
T |
8: 77,985,685 (GRCm39) |
|
probably null |
Het |
| Asap3 |
TGAGGAGGAGGAGGAGGA |
TGAGGAGGAGGAGGAGGAGGA |
4: 135,968,552 (GRCm39) |
|
probably benign |
Het |
| Bcap29 |
T |
C |
12: 31,667,151 (GRCm39) |
H170R |
probably benign |
Het |
| Bltp1 |
T |
A |
3: 37,041,730 (GRCm39) |
C2703S |
probably damaging |
Het |
| Brf1 |
T |
C |
12: 112,932,991 (GRCm39) |
|
probably null |
Het |
| Btnl7-ps |
T |
A |
17: 34,752,941 (GRCm39) |
|
noncoding transcript |
Het |
| Cdh12 |
C |
A |
15: 21,583,912 (GRCm39) |
T584K |
probably damaging |
Het |
| Col13a1 |
A |
G |
10: 61,703,608 (GRCm39) |
|
probably null |
Het |
| Csrp2 |
G |
A |
10: 110,773,735 (GRCm39) |
|
probably benign |
Het |
| Ctla2a |
T |
A |
13: 61,083,821 (GRCm39) |
D37V |
probably damaging |
Het |
| Cubn |
T |
A |
2: 13,355,754 (GRCm39) |
H1826L |
probably damaging |
Het |
| Dnajc19 |
A |
G |
3: 34,134,378 (GRCm39) |
|
probably null |
Het |
| Dxo |
T |
C |
17: 35,057,745 (GRCm39) |
|
probably benign |
Het |
| Edil3 |
A |
T |
13: 89,325,417 (GRCm39) |
M269L |
probably benign |
Het |
| Fbxl7 |
C |
A |
15: 26,543,841 (GRCm39) |
G269C |
probably damaging |
Het |
| Gpnmb |
T |
A |
6: 49,028,799 (GRCm39) |
I439N |
possibly damaging |
Het |
| Grm7 |
G |
T |
6: 110,623,309 (GRCm39) |
V161F |
probably damaging |
Het |
| Gtpbp3 |
T |
G |
8: 71,944,779 (GRCm39) |
S345A |
probably benign |
Het |
| Hnrnpul2 |
A |
G |
19: 8,801,773 (GRCm39) |
E327G |
probably damaging |
Het |
| Ifi207 |
A |
T |
1: 173,555,029 (GRCm39) |
Y884* |
probably null |
Het |
| Ifi47 |
T |
C |
11: 48,986,352 (GRCm39) |
S40P |
probably benign |
Het |
| Kcnq3 |
A |
G |
15: 65,893,588 (GRCm39) |
|
probably null |
Het |
| Kifc3 |
G |
A |
8: 95,830,656 (GRCm39) |
|
probably benign |
Het |
| Muc4 |
G |
C |
16: 32,753,919 (GRCm38) |
R1265P |
probably benign |
Het |
| Mug1 |
C |
T |
6: 121,865,515 (GRCm39) |
|
probably benign |
Het |
| Myh2 |
A |
G |
11: 67,080,427 (GRCm39) |
I1214V |
probably benign |
Het |
| Naa30 |
A |
G |
14: 49,425,059 (GRCm39) |
N337S |
probably benign |
Het |
| Nap1l3 |
A |
T |
X: 121,305,221 (GRCm39) |
I499N |
possibly damaging |
Het |
| Nfat5 |
T |
A |
8: 108,078,053 (GRCm39) |
|
probably benign |
Het |
| Nisch |
A |
G |
14: 30,898,702 (GRCm39) |
|
probably benign |
Het |
| Nt5c3 |
A |
G |
6: 56,860,652 (GRCm39) |
|
probably benign |
Het |
| Pklr |
C |
T |
3: 89,050,008 (GRCm39) |
R328C |
probably damaging |
Het |
| Prrc2c |
G |
A |
1: 162,538,260 (GRCm39) |
R457C |
probably damaging |
Het |
| Rab1a |
T |
G |
11: 20,174,506 (GRCm39) |
|
probably benign |
Het |
| Rasa3 |
A |
T |
8: 13,638,972 (GRCm39) |
D278E |
probably benign |
Het |
| Rdh8 |
C |
T |
9: 20,734,629 (GRCm39) |
P99S |
probably damaging |
Het |
| Snx9 |
T |
A |
17: 5,978,475 (GRCm39) |
|
probably null |
Het |
| Spns3 |
C |
T |
11: 72,390,356 (GRCm39) |
|
probably benign |
Het |
| Sympk |
A |
G |
7: 18,774,486 (GRCm39) |
Y421C |
probably damaging |
Het |
| Tas1r2 |
G |
A |
4: 139,394,729 (GRCm39) |
C495Y |
probably damaging |
Het |
| Tmem63a |
G |
A |
1: 180,790,679 (GRCm39) |
D446N |
possibly damaging |
Het |
| Tmprss15 |
T |
C |
16: 78,851,030 (GRCm39) |
|
probably null |
Het |
| Tox3 |
G |
T |
8: 90,975,533 (GRCm39) |
T366K |
possibly damaging |
Het |
| Trdmt1 |
T |
A |
2: 13,526,108 (GRCm39) |
Q170L |
probably benign |
Het |
| Ttn |
A |
T |
2: 76,565,752 (GRCm39) |
V28200D |
probably damaging |
Het |
| Zfp616 |
G |
A |
11: 73,974,145 (GRCm39) |
W138* |
probably null |
Het |
| Zfr2 |
T |
G |
10: 81,081,913 (GRCm39) |
V493G |
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 |
|
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'- ACTGTCCCCAAAGTCATAATGG -3'
(R):5'- TGTCTTGTGATACAATCATAGGGAC -3'
Sequencing Primer
(F):5'- TGTCCCCAAAGTCATAATGGATAGAG -3'
(R):5'- TGTGATACAATCATAGGGACAAACC -3'
|
| Posted On |
2015-01-23 |
Incidental Mutation