Incidental Mutation 'R0602:Col25a1'
| ID |
201518 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col25a1
|
| Ensembl Gene |
ENSMUSG00000058897 |
| Gene Name |
collagen, type XXV, alpha 1 |
| Synonyms |
2700062B08Rik |
| MMRRC Submission |
038791-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.136)
|
| Stock # |
R0602 (G1)
|
| Quality Score |
39 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
129973992-130393533 bp(+) (GRCm39) |
| Type of Mutation |
splice site (4 bp from exon) |
| DNA Base Change (assembly) |
A to G
at 130369063 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: 99.6%
- 3x: 99.1%
- 10x: 97.5%
- 20x: 94.7%
|
| Validation Efficiency |
95% (58/61) |
| 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: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 9430038I01Rik |
T |
C |
7: 136,978,090 (GRCm39) |
|
probably benign |
Het |
| Arih1 |
A |
G |
9: 59,302,154 (GRCm39) |
|
probably benign |
Het |
| Bcl9 |
T |
C |
3: 97,113,102 (GRCm39) |
I1118V |
probably benign |
Het |
| Cap1 |
T |
C |
4: 122,766,202 (GRCm39) |
E12G |
probably damaging |
Het |
| Ccdc168 |
T |
A |
1: 44,099,127 (GRCm39) |
K657I |
possibly damaging |
Het |
| Ccr2 |
A |
G |
9: 123,906,658 (GRCm39) |
I313V |
probably benign |
Het |
| Cd1d2 |
T |
C |
3: 86,895,110 (GRCm39) |
S161P |
probably benign |
Het |
| Cd226 |
C |
T |
18: 89,287,135 (GRCm39) |
T311I |
probably benign |
Het |
| Cspg4 |
T |
C |
9: 56,795,301 (GRCm39) |
F1012S |
probably damaging |
Het |
| Dnah7b |
A |
G |
1: 46,364,002 (GRCm39) |
M3541V |
probably damaging |
Het |
| Erbb2 |
G |
A |
11: 98,325,097 (GRCm39) |
V852M |
probably damaging |
Het |
| Fer1l6 |
A |
C |
15: 58,449,794 (GRCm39) |
T667P |
probably damaging |
Het |
| Gal3st2c |
A |
G |
1: 93,936,901 (GRCm39) |
Y282C |
probably damaging |
Het |
| Glp1r |
T |
C |
17: 31,128,201 (GRCm39) |
L60P |
probably benign |
Het |
| Gtf2h2 |
A |
G |
13: 100,605,533 (GRCm39) |
V358A |
probably benign |
Het |
| H2ac18 |
T |
C |
3: 96,152,866 (GRCm39) |
|
probably benign |
Het |
| Hephl1 |
T |
A |
9: 15,000,347 (GRCm39) |
I302F |
probably damaging |
Het |
| Lgi2 |
T |
C |
5: 52,711,765 (GRCm39) |
D185G |
probably damaging |
Het |
| Lrtm1 |
T |
C |
14: 28,744,179 (GRCm39) |
|
probably benign |
Het |
| Megf10 |
T |
G |
18: 57,395,172 (GRCm39) |
D511E |
probably damaging |
Het |
| Myo5c |
A |
G |
9: 75,173,478 (GRCm39) |
|
probably null |
Het |
| Nrbf2 |
G |
A |
10: 67,103,605 (GRCm39) |
T166M |
probably damaging |
Het |
| Nrm |
C |
A |
17: 36,175,156 (GRCm39) |
Y61* |
probably null |
Het |
| Ola1 |
A |
G |
2: 72,924,056 (GRCm39) |
Y368H |
probably damaging |
Het |
| Or52s1 |
A |
C |
7: 102,861,787 (GRCm39) |
H229P |
possibly damaging |
Het |
| Or9i1b |
A |
G |
19: 13,897,145 (GRCm39) |
T254A |
probably benign |
Het |
| Or9q2 |
T |
C |
19: 13,772,026 (GRCm39) |
|
probably null |
Het |
| Panx1 |
A |
G |
9: 14,921,500 (GRCm39) |
L125P |
probably damaging |
Het |
| Pappa2 |
A |
G |
1: 158,590,625 (GRCm39) |
|
probably benign |
Het |
| Parp6 |
A |
G |
9: 59,556,648 (GRCm39) |
|
probably benign |
Het |
| Pomgnt2 |
A |
G |
9: 121,811,339 (GRCm39) |
Y481H |
probably benign |
Het |
| Ppp4c |
A |
G |
7: 126,388,254 (GRCm39) |
|
probably benign |
Het |
| Prl8a8 |
T |
A |
13: 27,692,533 (GRCm39) |
|
probably benign |
Het |
| Prpf40b |
C |
A |
15: 99,202,352 (GRCm39) |
A70E |
unknown |
Het |
| Ptgfr |
G |
A |
3: 151,540,839 (GRCm39) |
T223M |
probably damaging |
Het |
| Ptprc |
C |
T |
1: 138,017,223 (GRCm39) |
|
probably benign |
Het |
| Rgs22 |
T |
C |
15: 36,140,018 (GRCm39) |
|
probably benign |
Het |
| Rpgrip1 |
A |
G |
14: 52,371,313 (GRCm39) |
E344G |
possibly damaging |
Het |
| Sgca |
A |
T |
11: 94,854,061 (GRCm39) |
I383N |
possibly damaging |
Het |
| Sgms2 |
T |
A |
3: 131,118,756 (GRCm39) |
|
probably null |
Het |
| Slc9b1 |
C |
A |
3: 135,103,516 (GRCm39) |
Q549K |
probably benign |
Het |
| Smc4 |
G |
C |
3: 68,916,871 (GRCm39) |
A187P |
probably damaging |
Het |
| Smco1 |
A |
G |
16: 32,092,062 (GRCm39) |
S47G |
probably damaging |
Het |
| Sobp |
T |
A |
10: 42,898,385 (GRCm39) |
E400V |
probably damaging |
Het |
| Sp140l1 |
C |
G |
1: 85,077,226 (GRCm39) |
K113N |
probably benign |
Het |
| Stil |
T |
A |
4: 114,881,620 (GRCm39) |
|
probably benign |
Het |
| Sult3a2 |
A |
T |
10: 33,658,044 (GRCm39) |
M23K |
probably benign |
Het |
| Syne2 |
AGAGTGAG |
AGAGTGAGTGAG |
12: 76,144,734 (GRCm39) |
|
probably null |
Het |
| Tcam1 |
G |
A |
11: 106,174,904 (GRCm39) |
E120K |
probably benign |
Het |
| Tcof1 |
C |
A |
18: 60,966,605 (GRCm39) |
G329W |
probably damaging |
Het |
| Ttc13 |
A |
T |
8: 125,401,105 (GRCm39) |
S624T |
probably damaging |
Het |
| Vmn1r171 |
G |
T |
7: 23,332,602 (GRCm39) |
V276L |
probably benign |
Het |
| Vps13b |
T |
C |
15: 35,422,514 (GRCm39) |
L158P |
probably damaging |
Het |
| Vps54 |
A |
G |
11: 21,256,434 (GRCm39) |
I634M |
possibly damaging |
Het |
| Vwa8 |
T |
G |
14: 79,258,060 (GRCm39) |
S736R |
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 |
|
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 |
|
|
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'- GCCATCATCTGTGGGGCATGTATTG -3'
(R):5'- TGGCAGCCCAGGCTAAACTTTC -3'
Sequencing Primer
(F):5'- TTGTAGCAATGTGATATTCATCCCAG -3'
(R):5'- CCAGGCTAAACTTTCGAGTTG -3'
|
| Posted On |
2014-06-18 |
Incidental Mutation