Incidental Mutation 'R6898:Col25a1'
| ID |
538442 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col25a1
|
| Ensembl Gene |
ENSMUSG00000058897 |
| Gene Name |
collagen, type XXV, alpha 1 |
| Synonyms |
2700062B08Rik |
| MMRRC Submission |
044992-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.136)
|
| Stock # |
R6898 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
129973992-130393533 bp(+) (GRCm39) |
| Type of Mutation |
critical splice donor site (2 bp from exon) |
| DNA Base Change (assembly) |
T to C
at 130378377 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000079210
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000080335]
[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 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: 100.0%
- 3x: 99.9%
- 10x: 99.2%
- 20x: 97.5%
|
| Validation Efficiency |
100% (46/46) |
| 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: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ankrd7 |
G |
T |
6: 18,868,100 (GRCm39) |
|
probably null |
Het |
| Aoc1l2 |
A |
T |
6: 48,907,975 (GRCm39) |
Y325F |
probably damaging |
Het |
| Aplnr |
A |
T |
2: 84,970,155 (GRCm39) |
|
probably benign |
Het |
| Capns2 |
T |
C |
8: 93,628,605 (GRCm39) |
S165P |
probably damaging |
Het |
| Crocc2 |
T |
C |
1: 93,143,304 (GRCm39) |
V1302A |
probably benign |
Het |
| Cul9 |
C |
A |
17: 46,821,952 (GRCm39) |
R1841M |
possibly damaging |
Het |
| Dnhd1 |
T |
C |
7: 105,336,584 (GRCm39) |
L1213P |
probably damaging |
Het |
| Dscam |
A |
T |
16: 96,631,100 (GRCm39) |
I305K |
probably benign |
Het |
| Dsp |
A |
G |
13: 38,376,193 (GRCm39) |
E1326G |
possibly damaging |
Het |
| Eif4a3l1 |
T |
A |
6: 136,305,617 (GRCm39) |
V26E |
probably benign |
Het |
| Emc9 |
A |
G |
14: 55,822,367 (GRCm39) |
|
probably null |
Het |
| Eppk1 |
A |
C |
15: 75,996,126 (GRCm39) |
S252A |
probably benign |
Het |
| Fn1 |
T |
A |
1: 71,639,572 (GRCm39) |
T1830S |
probably damaging |
Het |
| Fryl |
A |
T |
5: 73,179,485 (GRCm39) |
M2974K |
probably damaging |
Het |
| Gdpd3 |
C |
A |
7: 126,370,201 (GRCm39) |
S250* |
probably null |
Het |
| Gnl3 |
A |
T |
14: 30,735,136 (GRCm39) |
S485R |
probably benign |
Het |
| Gpt2 |
G |
A |
8: 86,244,681 (GRCm39) |
E325K |
probably benign |
Het |
| Hsd17b3 |
T |
C |
13: 64,207,339 (GRCm39) |
Y234C |
probably benign |
Het |
| Lima1 |
T |
C |
15: 99,679,148 (GRCm39) |
H271R |
possibly damaging |
Het |
| Nfu1 |
G |
A |
6: 86,994,034 (GRCm39) |
|
probably null |
Het |
| Noto |
A |
G |
6: 85,404,942 (GRCm39) |
E97G |
probably damaging |
Het |
| Ntng1 |
T |
C |
3: 109,779,534 (GRCm39) |
K348E |
probably damaging |
Het |
| Or2y13 |
G |
A |
11: 49,414,536 (GRCm39) |
|
probably benign |
Het |
| Or4a70 |
C |
T |
2: 89,324,594 (GRCm39) |
G21R |
possibly damaging |
Het |
| Osmr |
C |
A |
15: 6,845,364 (GRCm39) |
V801F |
probably damaging |
Het |
| Papln |
A |
G |
12: 83,824,234 (GRCm39) |
E554G |
probably benign |
Het |
| Pitrm1 |
T |
C |
13: 6,605,495 (GRCm39) |
L175P |
probably damaging |
Het |
| Pramel22 |
A |
T |
4: 143,382,053 (GRCm39) |
N214K |
probably damaging |
Het |
| Pramel7 |
T |
C |
2: 87,320,070 (GRCm39) |
T408A |
probably damaging |
Het |
| Serinc2 |
A |
T |
4: 130,149,235 (GRCm39) |
D322E |
probably benign |
Het |
| Setx |
T |
C |
2: 29,038,120 (GRCm39) |
V1535A |
probably benign |
Het |
| Sgce |
A |
T |
6: 4,689,666 (GRCm39) |
V389E |
probably damaging |
Het |
| Snx11 |
G |
A |
11: 96,659,888 (GRCm39) |
T267I |
probably benign |
Het |
| Spata6l |
T |
G |
19: 28,921,688 (GRCm39) |
Q146P |
probably benign |
Het |
| Specc1 |
G |
A |
11: 62,009,162 (GRCm39) |
S306N |
probably benign |
Het |
| Spocd1 |
A |
G |
4: 129,850,305 (GRCm39) |
|
probably benign |
Het |
| St7 |
T |
A |
6: 17,854,945 (GRCm39) |
V294D |
probably damaging |
Het |
| Stab1 |
C |
T |
14: 30,880,920 (GRCm39) |
R624Q |
probably benign |
Het |
| Tcf21 |
T |
C |
10: 22,695,403 (GRCm39) |
I134V |
probably benign |
Het |
| Tgfb2 |
T |
A |
1: 186,364,697 (GRCm39) |
I266F |
probably damaging |
Het |
| Tgfbr3l |
A |
G |
8: 4,300,365 (GRCm39) |
I209M |
possibly damaging |
Het |
| Tmcc3 |
A |
G |
10: 94,387,034 (GRCm39) |
|
probably null |
Het |
| Toe1 |
A |
G |
4: 116,664,671 (GRCm39) |
S16P |
probably damaging |
Het |
| Vps16 |
T |
C |
2: 130,279,601 (GRCm39) |
V38A |
possibly damaging |
Het |
| Wnk2 |
G |
T |
13: 49,224,557 (GRCm39) |
D1001E |
probably 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 |
|
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 |
|
|
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'- AATGTCACTAATGGAGAGGCC -3'
(R):5'- GTACCACTATGCAATGTCAGTTAC -3'
Sequencing Primer
(F):5'- ATGTCACTAATGGAGAGGCCTTTCC -3'
(R):5'- TGTGCACAGCACAGTAAG -3'
|
| Posted On |
2018-11-06 |
Incidental Mutation