Incidental Mutation 'R3818:Col25a1'
ID |
274770 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Col25a1
|
Ensembl Gene |
ENSMUSG00000058897 |
Gene Name |
collagen, type XXV, alpha 1 |
Synonyms |
2700062B08Rik |
MMRRC Submission |
040772-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.136)
|
Stock # |
R3818 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
129973992-130393533 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 130343720 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Lysine to Arginine
at position 396
(K396R)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000138875
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000080335]
[ENSMUST00000106353]
[ENSMUST00000183368]
|
AlphaFold |
Q99MQ5 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000080335
AA Change: K396R
PolyPhen 2
Score 0.221 (Sensitivity: 0.91; Specificity: 0.88)
|
SMART Domains |
Protein: ENSMUSP00000079210 Gene: ENSMUSG00000058897 AA Change: K396R
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
AA Change: K368R
PolyPhen 2
Score 0.074 (Sensitivity: 0.93; Specificity: 0.85)
|
SMART Domains |
Protein: ENSMUSP00000101960 Gene: ENSMUSG00000058897 AA Change: K368R
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 |
possibly damaging
Transcript: ENSMUST00000183368
AA Change: K396R
PolyPhen 2
Score 0.877 (Sensitivity: 0.83; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000138875 Gene: ENSMUSG00000058897 AA Change: K396R
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 |
0.0659 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.7%
- 20x: 96.4%
|
Validation Efficiency |
100% (34/34) |
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: 35 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
2310011J03Rik |
T |
C |
10: 80,155,351 (GRCm39) |
D54G |
probably damaging |
Het |
Adra2b |
G |
T |
2: 127,205,755 (GRCm39) |
E86* |
probably null |
Het |
Cachd1 |
A |
T |
4: 100,848,062 (GRCm39) |
D1059V |
probably damaging |
Het |
Cd177 |
A |
G |
7: 24,453,817 (GRCm39) |
V358A |
probably benign |
Het |
Csmd1 |
C |
T |
8: 16,052,522 (GRCm39) |
A2201T |
probably damaging |
Het |
Cyp4a12b |
A |
T |
4: 115,289,667 (GRCm39) |
D178V |
probably damaging |
Het |
Cyp4a30b |
G |
T |
4: 115,316,206 (GRCm39) |
A311S |
probably damaging |
Het |
Dse |
T |
C |
10: 34,029,429 (GRCm39) |
I554V |
probably benign |
Het |
Gabrg3 |
G |
A |
7: 57,031,412 (GRCm39) |
Q43* |
probably null |
Het |
Gjb2 |
A |
G |
14: 57,337,530 (GRCm39) |
V226A |
probably benign |
Het |
Gpr21 |
C |
A |
2: 37,408,324 (GRCm39) |
T290N |
probably damaging |
Het |
Gsdme |
A |
C |
6: 50,196,391 (GRCm39) |
S340A |
probably benign |
Het |
Hivep2 |
T |
C |
10: 14,019,685 (GRCm39) |
V2152A |
possibly damaging |
Het |
Mamdc4 |
C |
T |
2: 25,455,785 (GRCm39) |
S840N |
probably benign |
Het |
Or5p59 |
A |
G |
7: 107,702,705 (GRCm39) |
Y63C |
possibly damaging |
Het |
Or8i2 |
G |
A |
2: 86,852,054 (GRCm39) |
T278I |
probably benign |
Het |
Pah |
A |
G |
10: 87,357,866 (GRCm39) |
|
probably benign |
Het |
Pikfyve |
T |
A |
1: 65,284,917 (GRCm39) |
S794T |
probably damaging |
Het |
Plekhn1 |
T |
C |
4: 156,309,990 (GRCm39) |
H108R |
probably damaging |
Het |
Pomgnt1 |
T |
A |
4: 116,011,139 (GRCm39) |
|
probably null |
Het |
Prkd1 |
A |
T |
12: 50,466,667 (GRCm39) |
|
probably benign |
Het |
Pwp1 |
C |
T |
10: 85,723,993 (GRCm39) |
P498L |
possibly damaging |
Het |
Rasa4 |
A |
G |
5: 136,131,147 (GRCm39) |
T414A |
possibly damaging |
Het |
Rbm26 |
A |
T |
14: 105,378,706 (GRCm39) |
L594I |
probably damaging |
Het |
Rufy4 |
T |
C |
1: 74,186,822 (GRCm39) |
C537R |
probably damaging |
Het |
Skint5 |
A |
G |
4: 113,486,319 (GRCm39) |
|
probably benign |
Het |
Sorcs3 |
A |
G |
19: 48,592,343 (GRCm39) |
N336S |
probably benign |
Het |
Sspo |
A |
T |
6: 48,458,037 (GRCm39) |
E3269V |
possibly damaging |
Het |
Tlr4 |
A |
G |
4: 66,759,553 (GRCm39) |
E782G |
probably benign |
Het |
Tnfrsf11a |
C |
T |
1: 105,737,085 (GRCm39) |
T64I |
probably damaging |
Het |
Top2b |
T |
G |
14: 16,409,189 (GRCm38) |
I777M |
probably damaging |
Het |
Ttl |
T |
C |
2: 128,934,914 (GRCm39) |
V358A |
probably damaging |
Het |
Wdhd1 |
A |
G |
14: 47,481,258 (GRCm39) |
|
probably null |
Het |
Wdr37 |
A |
G |
13: 8,903,632 (GRCm39) |
|
probably benign |
Het |
Zfp939 |
T |
C |
7: 39,122,792 (GRCm39) |
|
noncoding transcript |
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 |
|
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'- AATGAGTCCCTGCTATGATGATATG -3'
(R):5'- CCTCTCTGAATGGAGTTAGGTAAC -3'
Sequencing Primer
(F):5'- TCCCTGCTATGATGATATGTATACTG -3'
(R):5'- AAGAACTGATTCCCACAGGTTCTCTG -3'
|
Posted On |
2015-04-02 |