Incidental Mutation 'R8524:Col25a1'
| ID |
658706 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col25a1
|
| Ensembl Gene |
ENSMUSG00000058897 |
| Gene Name |
collagen, type XXV, alpha 1 |
| Synonyms |
2700062B08Rik |
| MMRRC Submission |
067949-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.136)
|
| Stock # |
R8524 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
129973992-130393533 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 130342873 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Proline to Histidine
at position 350
(P350H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000101960
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000080335]
[ENSMUST00000106353]
[ENSMUST00000183368]
|
| AlphaFold |
Q99MQ5 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000080335
AA Change: P378H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000079210
Gene: ENSMUSG00000058897
AA Change: P378H
| 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 damaging
Transcript: ENSMUST00000106353
AA Change: P350H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000101960
Gene: ENSMUSG00000058897
AA Change: P350H
| 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 damaging
Transcript: ENSMUST00000183368
AA Change: P378H
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897
AA Change: P378H
| 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 |
0.1604 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.2%
|
| Validation Efficiency |
100% (41/41) |
| 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: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ccdc65 |
A |
T |
15: 98,606,990 (GRCm39) |
T66S |
probably benign |
Het |
| Cers1 |
G |
A |
8: 70,783,898 (GRCm39) |
G282D |
probably damaging |
Het |
| Cfap57 |
C |
T |
4: 118,472,128 (GRCm39) |
V84I |
probably benign |
Het |
| Coq5 |
T |
C |
5: 115,422,612 (GRCm39) |
I172T |
probably damaging |
Het |
| Dand5 |
A |
T |
8: 85,549,056 (GRCm39) |
L85* |
probably null |
Het |
| Dnah8 |
T |
A |
17: 30,934,472 (GRCm39) |
W1486R |
possibly damaging |
Het |
| Dpp8 |
T |
C |
9: 64,950,989 (GRCm39) |
Y142H |
probably damaging |
Het |
| G530012D18Rik |
C |
G |
1: 85,504,935 (GRCm39) |
D113E |
unknown |
Het |
| Gng7 |
T |
A |
10: 80,787,537 (GRCm39) |
H42L |
possibly damaging |
Het |
| Gps2 |
T |
C |
11: 69,805,832 (GRCm39) |
V93A |
probably damaging |
Het |
| Hspa9 |
T |
C |
18: 35,087,297 (GRCm39) |
S3G |
unknown |
Het |
| Impg2 |
A |
G |
16: 56,038,757 (GRCm39) |
N132D |
probably benign |
Het |
| Jak2 |
A |
T |
19: 29,273,105 (GRCm39) |
N643I |
probably damaging |
Het |
| Kcng2 |
T |
C |
18: 80,338,896 (GRCm39) |
D464G |
probably benign |
Het |
| Kdm4b |
T |
A |
17: 56,706,384 (GRCm39) |
C833S |
probably damaging |
Het |
| Ly86 |
G |
A |
13: 37,560,869 (GRCm39) |
D77N |
probably damaging |
Het |
| Map7 |
G |
A |
10: 20,142,569 (GRCm39) |
A330T |
probably benign |
Het |
| Mettl1 |
T |
C |
10: 126,877,908 (GRCm39) |
S21P |
probably damaging |
Het |
| Mga |
A |
G |
2: 119,771,997 (GRCm39) |
Y1540C |
probably damaging |
Het |
| Mpp4 |
A |
G |
1: 59,183,840 (GRCm39) |
L300P |
probably damaging |
Het |
| Mycbp2 |
A |
G |
14: 103,392,895 (GRCm39) |
M3222T |
probably benign |
Het |
| Nat8f6 |
A |
G |
6: 85,785,541 (GRCm39) |
Y203H |
probably benign |
Het |
| Nod1 |
C |
T |
6: 54,925,060 (GRCm39) |
E84K |
probably damaging |
Het |
| Or10v9 |
A |
G |
19: 11,832,445 (GRCm39) |
Y291H |
probably damaging |
Het |
| Or2b28 |
T |
C |
13: 21,531,248 (GRCm39) |
V50A |
probably benign |
Het |
| Or8k28 |
T |
C |
2: 86,285,961 (GRCm39) |
Y218C |
probably damaging |
Het |
| Padi2 |
A |
G |
4: 140,677,006 (GRCm39) |
N598S |
possibly damaging |
Het |
| Pclo |
C |
T |
5: 14,729,521 (GRCm39) |
|
probably benign |
Het |
| Pdik1l |
T |
G |
4: 134,013,921 (GRCm39) |
E12D |
probably benign |
Het |
| Plcg1 |
G |
A |
2: 160,603,387 (GRCm39) |
|
probably null |
Het |
| Rasgrf1 |
A |
G |
9: 89,797,638 (GRCm39) |
H172R |
possibly damaging |
Het |
| Rnf41 |
C |
G |
10: 128,271,299 (GRCm39) |
R70G |
possibly damaging |
Het |
| Rsbn1 |
A |
T |
3: 103,835,687 (GRCm39) |
K203* |
probably null |
Het |
| Setbp1 |
T |
C |
18: 78,901,969 (GRCm39) |
D566G |
probably damaging |
Het |
| Slc7a14 |
A |
C |
3: 31,278,282 (GRCm39) |
V441G |
possibly damaging |
Het |
| Sorl1 |
T |
A |
9: 41,885,370 (GRCm39) |
N2077I |
probably damaging |
Het |
| Spryd3 |
G |
A |
15: 102,026,583 (GRCm39) |
R363* |
probably null |
Het |
| St6galnac1 |
G |
T |
11: 116,658,547 (GRCm39) |
R306S |
possibly damaging |
Het |
| Tmem245 |
T |
C |
4: 56,906,261 (GRCm39) |
Q548R |
probably benign |
Het |
| Trim35 |
C |
T |
14: 66,544,493 (GRCm39) |
R276C |
probably damaging |
Het |
| Trim55 |
A |
T |
3: 19,725,113 (GRCm39) |
D210V |
probably benign |
Het |
| Tsg101 |
A |
T |
7: 46,542,115 (GRCm39) |
D279E |
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 |
|
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 |
|
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'- GTCGGTTTGTGCACATAGC -3'
(R):5'- TTGAACTGCAAAATCACTAGCC -3'
Sequencing Primer
(F):5'- CATAGCGGGATCAGTCATCTTCAG -3'
(R):5'- CACCAGTGTGCATTCCAATGAGG -3'
|
| Posted On |
2021-01-18 |
Incidental Mutation