Incidental Mutation 'R2902:Col25a1'
ID |
261492 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col25a1
|
Ensembl Gene |
ENSMUSG00000058897 |
Gene Name |
collagen, type XXV, alpha 1 |
Synonyms |
2700062B08Rik |
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.136)
|
Stock # |
R2902 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
3 |
Chromosomal Location |
129973992-130393533 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 130340040 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Glutamic Acid to Valine
at position 351
(E351V)
|
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: E351V
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000079210 Gene: ENSMUSG00000058897 AA Change: E351V
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: E323V
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
SMART Domains |
Protein: ENSMUSP00000101960 Gene: ENSMUSG00000058897 AA Change: E323V
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 damaging
Transcript: ENSMUST00000183368
AA Change: E351V
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000138875 Gene: ENSMUSG00000058897 AA Change: E351V
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 |
0.0994 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.8%
|
Validation Efficiency |
|
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 |
Apobec2 |
T |
C |
17: 48,730,409 (GRCm39) |
T86A |
probably benign |
Het |
C1qtnf1 |
A |
G |
11: 118,338,930 (GRCm39) |
|
probably null |
Het |
Cacng3 |
A |
G |
7: 122,353,750 (GRCm39) |
K78R |
possibly damaging |
Het |
Cep68 |
A |
G |
11: 20,190,187 (GRCm39) |
L275P |
probably damaging |
Het |
Chrm4 |
A |
G |
2: 91,758,302 (GRCm39) |
K237E |
probably benign |
Het |
Clvs1 |
A |
G |
4: 9,281,972 (GRCm39) |
K139E |
probably damaging |
Het |
Cyp4f18 |
A |
T |
8: 72,756,255 (GRCm39) |
I107N |
probably damaging |
Het |
Dagla |
A |
G |
19: 10,225,467 (GRCm39) |
L899P |
probably damaging |
Het |
Dnah3 |
T |
C |
7: 119,550,722 (GRCm39) |
K3199R |
possibly damaging |
Het |
Ecpas |
G |
A |
4: 58,809,691 (GRCm39) |
T1592M |
probably benign |
Het |
Emc10 |
G |
A |
7: 44,142,616 (GRCm39) |
R109W |
probably damaging |
Het |
Fam186a |
G |
T |
15: 99,843,049 (GRCm39) |
T1065K |
possibly damaging |
Het |
Ferd3l |
T |
G |
12: 33,978,952 (GRCm39) |
M155R |
probably damaging |
Het |
Fgd4 |
A |
G |
16: 16,243,729 (GRCm39) |
Y602H |
probably damaging |
Het |
Gldn |
T |
C |
9: 54,243,098 (GRCm39) |
L360P |
possibly damaging |
Het |
Gm9920 |
C |
A |
15: 54,975,867 (GRCm39) |
|
probably benign |
Het |
Inhbc |
T |
C |
10: 127,193,621 (GRCm39) |
T132A |
probably benign |
Het |
Krt23 |
T |
C |
11: 99,374,797 (GRCm39) |
D260G |
probably damaging |
Het |
Lrch3 |
G |
A |
16: 32,770,766 (GRCm39) |
A123T |
probably damaging |
Het |
Mark2 |
A |
T |
19: 7,260,813 (GRCm39) |
S408T |
probably benign |
Het |
Nme8 |
A |
T |
13: 19,859,834 (GRCm39) |
V23E |
probably benign |
Het |
Nod2 |
A |
T |
8: 89,402,091 (GRCm39) |
I912F |
probably damaging |
Het |
Nxpe4 |
A |
G |
9: 48,305,446 (GRCm39) |
I279V |
probably benign |
Het |
Oas3 |
A |
G |
5: 120,896,982 (GRCm39) |
F880L |
probably damaging |
Het |
Or5ak23 |
C |
T |
2: 85,244,396 (GRCm39) |
V276M |
possibly damaging |
Het |
Or6c6c |
A |
G |
10: 129,541,320 (GRCm39) |
H191R |
probably benign |
Het |
Or8c11 |
T |
A |
9: 38,289,337 (GRCm39) |
N53K |
possibly damaging |
Het |
Pcnt |
C |
T |
10: 76,211,064 (GRCm39) |
R2371H |
probably damaging |
Het |
Prex2 |
A |
T |
1: 11,278,838 (GRCm39) |
N1389I |
possibly damaging |
Het |
Prf1 |
A |
T |
10: 61,136,098 (GRCm39) |
N125Y |
probably damaging |
Het |
Prr12 |
C |
T |
7: 44,697,036 (GRCm39) |
G960R |
unknown |
Het |
Rap1b |
A |
G |
10: 117,660,507 (GRCm39) |
S17P |
probably damaging |
Het |
Rhot2 |
G |
T |
17: 26,062,950 (GRCm39) |
Q63K |
probably damaging |
Het |
Rnpepl1 |
C |
T |
1: 92,844,102 (GRCm39) |
L278F |
probably damaging |
Het |
Slco1a6 |
A |
G |
6: 142,042,046 (GRCm39) |
L510P |
probably damaging |
Het |
Ssc4d |
G |
A |
5: 135,993,517 (GRCm39) |
P113L |
possibly damaging |
Het |
Sv2a |
A |
T |
3: 96,101,072 (GRCm39) |
N690I |
possibly damaging |
Het |
Tbc1d24 |
T |
C |
17: 24,426,220 (GRCm39) |
Y452C |
probably benign |
Het |
Tmem132d |
G |
T |
5: 127,860,832 (GRCm39) |
H1096Q |
probably benign |
Het |
Tmem82 |
C |
A |
4: 141,343,775 (GRCm39) |
G165V |
probably benign |
Het |
Tpo |
T |
A |
12: 30,169,448 (GRCm39) |
T96S |
possibly damaging |
Het |
Triobp |
A |
G |
15: 78,857,618 (GRCm39) |
E1073G |
possibly damaging |
Het |
Tspoap1 |
C |
T |
11: 87,668,801 (GRCm39) |
P1358L |
probably benign |
Het |
Usp47 |
A |
G |
7: 111,692,658 (GRCm39) |
Y1020C |
probably damaging |
Het |
Washc4 |
C |
A |
10: 83,390,627 (GRCm39) |
Y153* |
probably null |
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 |
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'- TGGAGCTTTGCCCTAAATGTC -3'
(R):5'- TAGTGGTTCCTAAAGCTTCCTGG -3'
Sequencing Primer
(F):5'- TGCCCTAAATGTCCACTGATGAG -3'
(R):5'- ATAACTTCCAATTGCATGCCTGGG -3'
|
Posted On |
2015-01-23 |