Incidental Mutation 'R5110:Col25a1'
| ID |
393789 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col25a1
|
| Ensembl Gene |
ENSMUSG00000058897 |
| Gene Name |
collagen, type XXV, alpha 1 |
| Synonyms |
2700062B08Rik |
| MMRRC Submission |
042698-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.136)
|
| Stock # |
R5110 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
129973992-130393533 bp(+) (GRCm39) |
| Type of Mutation |
makesense |
| DNA Base Change (assembly) |
A to G
at 130378374 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Stop codon to Tryptophan
at position 594
(*594W)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000138875
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000080335]
[ENSMUST00000106353]
[ENSMUST00000183368]
|
| AlphaFold |
Q99MQ5 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000080335
AA Change: D609G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000079210
Gene: ENSMUSG00000058897
AA Change: D609G
| 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 null
Transcript: ENSMUST00000183368
AA Change: *594W
|
| SMART Domains |
Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897
AA Change: *594W
| 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: 99.0%
- 3x: 98.2%
- 10x: 95.9%
- 20x: 91.1%
|
| Validation Efficiency |
100% (61/61) |
| 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 |
|---|
| 2010315B03Rik |
C |
A |
9: 124,057,987 (GRCm39) |
|
probably null |
Het |
| 2310016G11Rik |
G |
A |
7: 44,327,286 (GRCm39) |
|
noncoding transcript |
Het |
| Abi2 |
G |
A |
1: 60,489,280 (GRCm39) |
V98I |
probably benign |
Het |
| Adam21 |
T |
C |
12: 81,606,989 (GRCm39) |
T258A |
probably benign |
Het |
| Adam33 |
A |
T |
2: 130,895,690 (GRCm39) |
C542S |
probably damaging |
Het |
| Adamts15 |
A |
G |
9: 30,832,740 (GRCm39) |
V265A |
probably benign |
Het |
| Ahnak |
A |
T |
19: 8,992,123 (GRCm39) |
D4469V |
probably damaging |
Het |
| Aicda |
A |
G |
6: 122,538,144 (GRCm39) |
N101D |
probably benign |
Het |
| Als2 |
A |
T |
1: 59,224,600 (GRCm39) |
D1040E |
probably damaging |
Het |
| Car15 |
T |
C |
16: 17,653,211 (GRCm39) |
R319G |
possibly damaging |
Het |
| Cdc23 |
C |
A |
18: 34,784,742 (GRCm39) |
V7L |
unknown |
Het |
| Col1a1 |
T |
C |
11: 94,832,419 (GRCm39) |
|
probably null |
Het |
| Cwf19l2 |
A |
G |
9: 3,450,012 (GRCm39) |
|
probably null |
Het |
| Dctn4 |
C |
T |
18: 60,679,387 (GRCm39) |
P236S |
probably damaging |
Het |
| Dennd2b |
A |
G |
7: 109,141,697 (GRCm39) |
S556P |
probably benign |
Het |
| Ehmt1 |
C |
A |
2: 24,742,802 (GRCm39) |
C459F |
probably benign |
Het |
| Enox1 |
T |
C |
14: 77,945,127 (GRCm39) |
|
probably null |
Het |
| Fam136b-ps |
A |
G |
15: 31,276,856 (GRCm39) |
|
probably benign |
Het |
| Fzd1 |
T |
C |
5: 4,806,448 (GRCm39) |
D378G |
probably benign |
Het |
| Golga5 |
G |
A |
12: 102,438,336 (GRCm39) |
R17Q |
probably benign |
Het |
| Hk1 |
A |
T |
10: 62,122,430 (GRCm39) |
Y422N |
probably damaging |
Het |
| Hsf4 |
A |
G |
8: 105,999,427 (GRCm39) |
D255G |
probably benign |
Het |
| Ift81 |
A |
G |
5: 122,689,121 (GRCm39) |
V665A |
probably benign |
Het |
| Igkv13-84 |
T |
C |
6: 68,916,592 (GRCm39) |
F3L |
probably benign |
Het |
| Kcnh1 |
T |
A |
1: 192,020,055 (GRCm39) |
S433R |
possibly damaging |
Het |
| Ktn1 |
A |
G |
14: 47,941,744 (GRCm39) |
|
probably benign |
Het |
| Lrp4 |
A |
T |
2: 91,327,417 (GRCm39) |
D1471V |
possibly damaging |
Het |
| Macf1 |
A |
T |
4: 123,261,801 (GRCm39) |
D6990E |
probably damaging |
Het |
| Map3k6 |
G |
A |
4: 132,974,859 (GRCm39) |
|
probably benign |
Het |
| Miox |
T |
A |
15: 89,219,759 (GRCm39) |
D82E |
probably benign |
Het |
| Or4n5 |
T |
G |
14: 50,133,032 (GRCm39) |
I76L |
possibly damaging |
Het |
| Ovgp1 |
G |
C |
3: 105,885,099 (GRCm39) |
R133P |
probably damaging |
Het |
| Per2 |
G |
A |
1: 91,357,237 (GRCm39) |
T642I |
possibly damaging |
Het |
| Pparg |
T |
C |
6: 115,449,964 (GRCm39) |
V321A |
probably damaging |
Het |
| Pptc7 |
T |
A |
5: 122,446,312 (GRCm39) |
N17K |
probably benign |
Het |
| Prpf19 |
T |
C |
19: 10,876,651 (GRCm39) |
|
probably benign |
Het |
| Rai14 |
T |
C |
15: 10,690,496 (GRCm39) |
|
probably benign |
Het |
| Sardh |
T |
C |
2: 27,079,559 (GRCm39) |
D911G |
probably benign |
Het |
| Sbf2 |
T |
A |
7: 109,963,864 (GRCm39) |
T994S |
probably benign |
Het |
| Slc1a1 |
G |
A |
19: 28,889,208 (GRCm39) |
E494K |
probably benign |
Het |
| Smarcc1 |
A |
G |
9: 110,026,852 (GRCm39) |
K771E |
possibly damaging |
Het |
| Stim1 |
T |
C |
7: 101,917,629 (GRCm39) |
V3A |
unknown |
Het |
| Syne3 |
G |
A |
12: 104,909,629 (GRCm39) |
R736C |
probably benign |
Het |
| Synj2 |
T |
C |
17: 6,087,990 (GRCm39) |
V986A |
probably benign |
Het |
| Tinag |
A |
G |
9: 76,859,289 (GRCm39) |
S440P |
probably damaging |
Het |
| Tshz2 |
A |
G |
2: 169,726,117 (GRCm39) |
T238A |
possibly damaging |
Het |
| Ttc8 |
T |
C |
12: 98,908,562 (GRCm39) |
M17T |
probably benign |
Het |
| Tubgcp5 |
G |
A |
7: 55,458,385 (GRCm39) |
R432Q |
probably damaging |
Het |
| Ugt1a10 |
T |
A |
1: 87,983,974 (GRCm39) |
|
probably null |
Het |
| Usp4 |
T |
A |
9: 108,239,877 (GRCm39) |
I202N |
probably damaging |
Het |
| Vmn1r194 |
T |
G |
13: 22,429,170 (GRCm39) |
S262R |
probably benign |
Het |
| Vmn2r101 |
T |
C |
17: 19,831,897 (GRCm39) |
F631S |
possibly damaging |
Het |
| Vps13b |
T |
A |
15: 35,770,955 (GRCm39) |
S2133T |
probably damaging |
Het |
| Zfp13 |
C |
A |
17: 23,799,834 (GRCm39) |
V77F |
probably benign |
Het |
| Zscan10 |
T |
A |
17: 23,828,606 (GRCm39) |
C306S |
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 |
|
|
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'- ACAGTCCCCTCACTTGATTAAAG -3'
(R):5'- GCCGATGTTGAGTGTCCTTAAC -3'
Sequencing Primer
(F):5'- CCCCTCACTTGATTAAAGAAATGTC -3'
(R):5'- GAAAGTACCACTATGCAATGTCAG -3'
|
| Posted On |
2016-06-15 |
Incidental Mutation