Incidental Mutation 'R5686:Col25a1'
| ID |
443342 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col25a1
|
| Ensembl Gene |
ENSMUSG00000058897 |
| Gene Name |
collagen, type XXV, alpha 1 |
| Synonyms |
2700062B08Rik |
| MMRRC Submission |
043319-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.136)
|
| Stock # |
R5686 (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 130357803 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 477
(E477G)
|
| 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: E477G
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000079210
Gene: ENSMUSG00000058897
AA Change: E477G
| 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: E449G
PolyPhen 2
Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000101960
Gene: ENSMUSG00000058897
AA Change: E449G
| 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: E477G
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897
AA Change: E477G
| 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: ENSMUST00000196901
|
| Meta Mutation Damage Score |
0.1115 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.7%
- 10x: 97.2%
- 20x: 95.1%
|
| Validation Efficiency |
97% (73/75) |
| 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: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2210408I21Rik |
A |
G |
13: 77,451,433 (GRCm39) |
E839G |
possibly damaging |
Het |
| Adgrf3 |
T |
A |
5: 30,402,304 (GRCm39) |
T575S |
probably damaging |
Het |
| Akap9 |
T |
A |
5: 4,021,926 (GRCm39) |
C1158S |
probably benign |
Het |
| Arhgap39 |
A |
G |
15: 76,610,833 (GRCm39) |
F926L |
probably damaging |
Het |
| BC035947 |
G |
T |
1: 78,474,567 (GRCm39) |
T655K |
probably benign |
Het |
| Bcas1 |
T |
C |
2: 170,248,730 (GRCm39) |
T64A |
probably benign |
Het |
| Bltp1 |
T |
A |
3: 36,971,809 (GRCm39) |
F514Y |
probably benign |
Het |
| Brca2 |
A |
G |
5: 150,464,369 (GRCm39) |
K1378E |
probably benign |
Het |
| Card6 |
A |
T |
15: 5,130,435 (GRCm39) |
N320K |
probably damaging |
Het |
| Ccdc3 |
A |
T |
2: 5,142,871 (GRCm39) |
I43F |
probably damaging |
Het |
| Cd200r1 |
T |
C |
16: 44,610,527 (GRCm39) |
S212P |
probably damaging |
Het |
| Cdh8 |
T |
C |
8: 99,759,854 (GRCm39) |
I632V |
probably benign |
Het |
| Cpne5 |
A |
T |
17: 29,402,991 (GRCm39) |
C215S |
possibly damaging |
Het |
| Crim1 |
T |
A |
17: 78,681,512 (GRCm39) |
S989T |
possibly damaging |
Het |
| Dnhd1 |
G |
A |
7: 105,352,416 (GRCm39) |
R2523Q |
probably damaging |
Het |
| Dync1h1 |
T |
A |
12: 110,582,838 (GRCm39) |
N340K |
probably benign |
Het |
| Eif4e2 |
G |
A |
1: 87,153,960 (GRCm39) |
|
probably null |
Het |
| Ephb6 |
G |
T |
6: 41,596,638 (GRCm39) |
R895L |
possibly damaging |
Het |
| Esrrg |
T |
A |
1: 187,882,395 (GRCm39) |
H217Q |
probably benign |
Het |
| Fgl1 |
T |
A |
8: 41,653,594 (GRCm39) |
K100* |
probably null |
Het |
| Flt4 |
T |
C |
11: 49,521,430 (GRCm39) |
V450A |
probably benign |
Het |
| G6pc2 |
A |
T |
2: 69,051,128 (GRCm39) |
I74L |
probably benign |
Het |
| Gabrr1 |
T |
C |
4: 33,161,684 (GRCm39) |
M336T |
probably damaging |
Het |
| Gli1 |
T |
A |
10: 127,173,305 (GRCm39) |
T118S |
probably benign |
Het |
| Gm5435 |
A |
T |
12: 82,542,800 (GRCm39) |
|
noncoding transcript |
Het |
| Got1l1 |
A |
G |
8: 27,688,087 (GRCm39) |
L314P |
probably damaging |
Het |
| Hk3 |
T |
A |
13: 55,154,626 (GRCm39) |
I740F |
probably damaging |
Het |
| Htr7 |
C |
A |
19: 35,947,271 (GRCm39) |
A248S |
probably damaging |
Het |
| Igsf9b |
A |
G |
9: 27,235,475 (GRCm39) |
T508A |
probably damaging |
Het |
| Il16 |
T |
A |
7: 83,297,936 (GRCm39) |
N431I |
probably benign |
Het |
| Lax1 |
G |
A |
1: 133,607,914 (GRCm39) |
P276S |
probably damaging |
Het |
| Lrp2 |
A |
T |
2: 69,341,405 (GRCm39) |
V925E |
possibly damaging |
Het |
| Lrp3 |
T |
A |
7: 34,902,910 (GRCm39) |
T479S |
possibly damaging |
Het |
| Metrn |
G |
A |
17: 26,014,191 (GRCm39) |
R212C |
probably damaging |
Het |
| Mlip |
A |
C |
9: 77,254,975 (GRCm39) |
|
probably null |
Het |
| Mmp24 |
C |
T |
2: 155,641,697 (GRCm39) |
T175I |
probably damaging |
Het |
| N6amt1 |
A |
T |
16: 87,151,223 (GRCm39) |
D28V |
probably damaging |
Het |
| Or1e21 |
A |
T |
11: 73,344,677 (GRCm39) |
Y120* |
probably null |
Het |
| Or4f4b |
G |
A |
2: 111,314,488 (GRCm39) |
G238R |
probably damaging |
Het |
| Or5p52 |
A |
G |
7: 107,502,119 (GRCm39) |
H65R |
probably damaging |
Het |
| Or5p66 |
G |
T |
7: 107,885,949 (GRCm39) |
A128E |
probably damaging |
Het |
| Or6d15 |
T |
C |
6: 116,559,890 (GRCm39) |
T6A |
probably benign |
Het |
| Or8b12i |
T |
A |
9: 20,082,265 (GRCm39) |
I201F |
possibly damaging |
Het |
| Pcdh17 |
T |
A |
14: 84,770,433 (GRCm39) |
N970K |
probably damaging |
Het |
| Pdzrn3 |
T |
C |
6: 101,128,389 (GRCm39) |
Y759C |
probably damaging |
Het |
| Pkd2l2 |
T |
C |
18: 34,558,290 (GRCm39) |
L323P |
probably damaging |
Het |
| Psg21 |
G |
T |
7: 18,386,183 (GRCm39) |
|
probably benign |
Het |
| Rest |
T |
C |
5: 77,429,573 (GRCm39) |
V664A |
probably benign |
Het |
| Sco2 |
G |
A |
15: 89,256,175 (GRCm39) |
R160* |
probably null |
Het |
| Sfswap |
T |
A |
5: 129,591,882 (GRCm39) |
S300T |
probably damaging |
Het |
| Slc5a10 |
A |
T |
11: 61,569,392 (GRCm39) |
M329K |
probably benign |
Het |
| Slco1a5 |
G |
A |
6: 142,182,033 (GRCm39) |
P564S |
probably damaging |
Het |
| Stk38 |
A |
G |
17: 29,201,103 (GRCm39) |
F191S |
probably damaging |
Het |
| Svep1 |
T |
A |
4: 58,072,826 (GRCm39) |
Y2161F |
possibly damaging |
Het |
| Tada2a |
G |
A |
11: 83,970,428 (GRCm39) |
T441M |
possibly damaging |
Het |
| Tg |
T |
A |
15: 66,560,738 (GRCm39) |
N1033K |
probably benign |
Het |
| Thoc3 |
A |
T |
13: 54,615,686 (GRCm39) |
I126N |
probably damaging |
Het |
| Tnc |
T |
C |
4: 63,925,967 (GRCm39) |
|
probably null |
Het |
| Tnc |
A |
T |
4: 63,927,032 (GRCm39) |
D831E |
possibly damaging |
Het |
| Uhmk1 |
A |
T |
1: 170,038,787 (GRCm39) |
V100E |
probably damaging |
Het |
| Usp43 |
G |
A |
11: 67,812,742 (GRCm39) |
|
probably benign |
Het |
| Vmn2r90 |
A |
T |
17: 17,933,712 (GRCm39) |
Y424F |
probably benign |
Het |
| Vps33a |
C |
T |
5: 123,685,064 (GRCm39) |
|
probably null |
Het |
| Xirp2 |
A |
T |
2: 67,312,642 (GRCm39) |
K37I |
probably damaging |
Het |
| Zfp106 |
A |
T |
2: 120,363,988 (GRCm39) |
|
probably null |
Het |
| Zfp748 |
A |
T |
13: 67,690,647 (GRCm39) |
C204* |
probably null |
Het |
| Zfp998 |
T |
C |
13: 66,579,722 (GRCm39) |
R254G |
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 |
|
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'- GTAGGACTTGGCTAGCCATTAC -3'
(R):5'- ATCTGTTGAGGTAGACTGATAGGTC -3'
Sequencing Primer
(F):5'- GCACAATCCTCAAGAAAGATTTTTCC -3'
(R):5'- ACATAGCTTTACATTTCTACCAACC -3'
|
| Posted On |
2016-11-09 |
Incidental Mutation