Incidental Mutation 'R3947:Col4a3'
| ID |
307739 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col4a3
|
| Ensembl Gene |
ENSMUSG00000079465 |
| Gene Name |
collagen, type IV, alpha 3 |
| Synonyms |
tumstatin, alpha3(IV) |
| MMRRC Submission |
040927-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R3947 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
82564647-82699778 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 82693053 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 1446
(I1446N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000109084
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000113457]
[ENSMUST00000125563]
[ENSMUST00000152664]
|
| AlphaFold |
Q9QZS0 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000113457
AA Change: I1446N
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000109084
Gene: ENSMUSG00000079465
AA Change: I1446N
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
28 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
41 |
102 |
9.6e-11 |
PFAM |
|
Pfam:Collagen
|
97 |
164 |
3.6e-11 |
PFAM |
|
Pfam:Collagen
|
164 |
223 |
3.6e-9 |
PFAM |
|
low complexity region
|
233 |
243 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
284 |
344 |
2.4e-10 |
PFAM |
|
low complexity region
|
368 |
393 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
415 |
477 |
5e-10 |
PFAM |
|
Pfam:Collagen
|
481 |
545 |
1e-9 |
PFAM |
|
low complexity region
|
550 |
585 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
588 |
653 |
8.9e-9 |
PFAM |
|
Pfam:Collagen
|
682 |
744 |
1.1e-8 |
PFAM |
|
Pfam:Collagen
|
743 |
807 |
6.9e-10 |
PFAM |
|
Pfam:Collagen
|
786 |
847 |
1.5e-8 |
PFAM |
|
Pfam:Collagen
|
845 |
904 |
1.5e-10 |
PFAM |
|
Pfam:Collagen
|
887 |
946 |
4.1e-10 |
PFAM |
|
Pfam:Collagen
|
948 |
1006 |
8.1e-11 |
PFAM |
|
Pfam:Collagen
|
997 |
1061 |
2.8e-10 |
PFAM |
|
Pfam:Collagen
|
1057 |
1120 |
2.5e-10 |
PFAM |
|
Pfam:Collagen
|
1114 |
1176 |
1.7e-9 |
PFAM |
|
Pfam:Collagen
|
1174 |
1233 |
1.1e-9 |
PFAM |
|
Pfam:Collagen
|
1232 |
1295 |
6.9e-9 |
PFAM |
|
low complexity region
|
1326 |
1347 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
1377 |
1439 |
4.9e-11 |
PFAM |
|
C4
|
1444 |
1553 |
3.77e-70 |
SMART |
|
C4
|
1554 |
1667 |
3.28e-70 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000125563
AA Change: I10N
PolyPhen 2
Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000137944
Gene: ENSMUSG00000079465
AA Change: I10N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:C4
|
8 |
60 |
4.7e-18 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000152664
AA Change: I10N
PolyPhen 2
Score 0.939 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000119094
Gene: ENSMUSG00000079465
AA Change: I10N
| Domain | Start | End | E-Value | Type |
|---|
|
C4
|
8 |
117 |
3.77e-70 |
SMART |
|
Pfam:C4
|
118 |
169 |
4.1e-14 |
PFAM |
|
low complexity region
|
185 |
196 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000181720
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000186858
|
| Meta Mutation Damage Score |
0.6467 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.4%
|
| Validation Efficiency |
97% (32/33) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Type IV collagen, the major structural component of basement membranes, is a multimeric protein composed of 3 alpha subunits. These subunits are encoded by 6 different genes, alpha 1 through alpha 6, each of which can form a triple helix structure with 2 other subunits to form type IV collagen. This gene encodes alpha 3. In the Goodpasture syndrome, autoantibodies bind to the collagen molecules in the basement membranes of alveoli and glomeruli. The epitopes that elicit these autoantibodies are localized largely to the non-collagenous C-terminal domain of the protein. A specific kinase phosphorylates amino acids in this same C-terminal region and the expression of this kinase is upregulated during pathogenesis. This gene is also linked to an autosomal recessive form of Alport syndrome. The mutations contributing to this syndrome are also located within the exons that encode this C-terminal region. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. [provided by RefSeq, Jun 2010]
PHENOTYPE: Homozygotes for targeted null mutations exhibit renal pathology including reduced glomerular filtration, impaired glomerular integrity, and glomerulonephrosis, resulting in uremia, proteinuria, and high mortality in young adults. Auditory thresholds aremildly increased across all test frequencies. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 33 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acin1 |
T |
A |
14: 54,916,790 (GRCm39) |
Q133L |
possibly damaging |
Het |
| Adgrg4 |
C |
T |
X: 55,963,114 (GRCm39) |
T1561I |
probably benign |
Het |
| Avl9 |
T |
C |
6: 56,705,650 (GRCm39) |
|
probably null |
Het |
| C87436 |
T |
A |
6: 86,423,168 (GRCm39) |
H247Q |
probably damaging |
Het |
| Cfap43 |
G |
T |
19: 47,754,418 (GRCm39) |
H969N |
probably benign |
Het |
| Chst15 |
T |
A |
7: 131,849,604 (GRCm39) |
N446Y |
probably damaging |
Het |
| Disc1 |
A |
G |
8: 125,814,874 (GRCm39) |
E246G |
probably damaging |
Het |
| Dyrk4 |
A |
G |
6: 126,862,268 (GRCm39) |
I408T |
probably damaging |
Het |
| Fnbp1l |
G |
T |
3: 122,338,228 (GRCm39) |
A481D |
possibly damaging |
Het |
| Gm10608 |
TACACACACACACACACACACACACACACACACACACACACACACACACACACACA |
TACACACACACACACACACACACACACACACACACACACACACACACACA |
9: 118,989,730 (GRCm39) |
|
probably benign |
Het |
| Grk2 |
G |
A |
19: 4,342,445 (GRCm39) |
T129M |
possibly damaging |
Het |
| Ino80d |
G |
T |
1: 63,113,662 (GRCm39) |
Q263K |
probably benign |
Het |
| Iqsec3 |
A |
T |
6: 121,364,783 (GRCm39) |
Y835* |
probably null |
Het |
| Irak3 |
T |
A |
10: 120,006,278 (GRCm39) |
M213L |
probably benign |
Het |
| Macf1 |
T |
C |
4: 123,274,213 (GRCm39) |
R6388G |
probably damaging |
Het |
| Mtnr1a |
T |
C |
8: 45,540,557 (GRCm39) |
Y173H |
probably damaging |
Het |
| Myo5b |
C |
T |
18: 74,828,474 (GRCm39) |
R709W |
probably damaging |
Het |
| Nebl |
A |
T |
2: 17,382,917 (GRCm39) |
|
probably null |
Het |
| Obscn |
T |
C |
11: 59,022,472 (GRCm39) |
R758G |
possibly damaging |
Het |
| Or2g1 |
A |
T |
17: 38,107,006 (GRCm39) |
I224L |
probably benign |
Het |
| Pex11g |
G |
A |
8: 3,515,787 (GRCm39) |
T82I |
probably benign |
Het |
| Pgr |
A |
G |
9: 8,961,453 (GRCm39) |
I842V |
probably benign |
Het |
| Pkd1 |
T |
A |
17: 24,797,011 (GRCm39) |
|
probably benign |
Het |
| Rbm20 |
T |
C |
19: 53,801,768 (GRCm39) |
I92T |
probably benign |
Het |
| Ryr3 |
C |
G |
2: 112,506,218 (GRCm39) |
R3443P |
probably damaging |
Het |
| Ssh2 |
A |
G |
11: 77,289,082 (GRCm39) |
D88G |
probably damaging |
Het |
| Suclg2 |
G |
T |
6: 95,556,219 (GRCm39) |
|
probably null |
Het |
| Tdrd3 |
A |
T |
14: 87,744,035 (GRCm39) |
D655V |
probably damaging |
Het |
| Tex2 |
C |
T |
11: 106,410,829 (GRCm39) |
D896N |
unknown |
Het |
| Tmem168 |
C |
A |
6: 13,583,051 (GRCm39) |
R610L |
probably damaging |
Het |
| Ttc17 |
A |
G |
2: 94,206,491 (GRCm39) |
|
probably benign |
Het |
| Vmn2r99 |
T |
C |
17: 19,599,252 (GRCm39) |
M312T |
probably benign |
Het |
| Wdfy3 |
T |
C |
5: 102,017,902 (GRCm39) |
E2546G |
probably damaging |
Het |
|
| Other mutations in Col4a3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00693:Col4a3
|
APN |
1 |
82,675,475 (GRCm39) |
missense |
unknown |
|
|
IGL00847:Col4a3
|
APN |
1 |
82,695,590 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01011:Col4a3
|
APN |
1 |
82,660,022 (GRCm39) |
missense |
unknown |
|
|
IGL01102:Col4a3
|
APN |
1 |
82,647,976 (GRCm39) |
missense |
unknown |
|
|
IGL01102:Col4a3
|
APN |
1 |
82,647,441 (GRCm39) |
missense |
unknown |
|
|
IGL02071:Col4a3
|
APN |
1 |
82,638,608 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02244:Col4a3
|
APN |
1 |
82,647,492 (GRCm39) |
splice site |
probably benign |
|
|
IGL02380:Col4a3
|
APN |
1 |
82,650,509 (GRCm39) |
splice site |
probably benign |
|
|
IGL02431:Col4a3
|
APN |
1 |
82,657,344 (GRCm39) |
nonsense |
probably null |
|
|
IGL02466:Col4a3
|
APN |
1 |
82,647,913 (GRCm39) |
missense |
unknown |
|
|
IGL02694:Col4a3
|
APN |
1 |
82,688,515 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02709:Col4a3
|
APN |
1 |
82,656,833 (GRCm39) |
missense |
unknown |
|
|
IGL02752:Col4a3
|
APN |
1 |
82,637,946 (GRCm39) |
missense |
unknown |
|
|
IGL02792:Col4a3
|
APN |
1 |
82,696,524 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03203:Col4a3
|
APN |
1 |
82,650,360 (GRCm39) |
nonsense |
probably null |
|
|
IGL03218:Col4a3
|
APN |
1 |
82,620,927 (GRCm39) |
splice site |
probably benign |
|
|
FR4976:Col4a3
|
UTSW |
1 |
82,696,627 (GRCm39) |
frame shift |
probably null |
|
|
PIT4260001:Col4a3
|
UTSW |
1 |
82,660,482 (GRCm39) |
missense |
unknown |
|
|
PIT4515001:Col4a3
|
UTSW |
1 |
82,660,024 (GRCm39) |
missense |
unknown |
|
|
R0035:Col4a3
|
UTSW |
1 |
82,650,474 (GRCm39) |
missense |
unknown |
|
|
R0099:Col4a3
|
UTSW |
1 |
82,695,714 (GRCm39) |
missense |
probably benign |
0.41 |
|
R0433:Col4a3
|
UTSW |
1 |
82,647,940 (GRCm39) |
missense |
unknown |
|
|
R0573:Col4a3
|
UTSW |
1 |
82,694,084 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R0606:Col4a3
|
UTSW |
1 |
82,650,307 (GRCm39) |
splice site |
probably benign |
|
|
R0715:Col4a3
|
UTSW |
1 |
82,629,879 (GRCm39) |
splice site |
probably benign |
|
|
R0961:Col4a3
|
UTSW |
1 |
82,686,297 (GRCm39) |
splice site |
probably benign |
|
|
R1257:Col4a3
|
UTSW |
1 |
82,694,086 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1264:Col4a3
|
UTSW |
1 |
82,621,022 (GRCm39) |
splice site |
probably benign |
|
|
R1373:Col4a3
|
UTSW |
1 |
82,667,808 (GRCm39) |
splice site |
probably benign |
|
|
R1694:Col4a3
|
UTSW |
1 |
82,668,384 (GRCm39) |
splice site |
probably null |
|
|
R1895:Col4a3
|
UTSW |
1 |
82,656,829 (GRCm39) |
missense |
unknown |
|
|
R1925:Col4a3
|
UTSW |
1 |
82,689,595 (GRCm39) |
unclassified |
probably benign |
|
|
R1925:Col4a3
|
UTSW |
1 |
82,678,094 (GRCm39) |
missense |
unknown |
|
|
R2033:Col4a3
|
UTSW |
1 |
82,695,732 (GRCm39) |
intron |
probably benign |
|
|
R2044:Col4a3
|
UTSW |
1 |
82,674,040 (GRCm39) |
missense |
unknown |
|
|
R2122:Col4a3
|
UTSW |
1 |
82,632,678 (GRCm39) |
missense |
unknown |
|
|
R2282:Col4a3
|
UTSW |
1 |
82,686,359 (GRCm39) |
missense |
unknown |
|
|
R2318:Col4a3
|
UTSW |
1 |
82,626,290 (GRCm39) |
splice site |
probably null |
|
|
R2421:Col4a3
|
UTSW |
1 |
82,647,996 (GRCm39) |
splice site |
probably benign |
|
|
R2517:Col4a3
|
UTSW |
1 |
82,658,431 (GRCm39) |
missense |
unknown |
|
|
R2965:Col4a3
|
UTSW |
1 |
82,626,321 (GRCm39) |
missense |
unknown |
|
|
R3085:Col4a3
|
UTSW |
1 |
82,628,979 (GRCm39) |
missense |
unknown |
|
|
R3150:Col4a3
|
UTSW |
1 |
82,634,858 (GRCm39) |
splice site |
probably null |
|
|
R4756:Col4a3
|
UTSW |
1 |
82,694,018 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R4910:Col4a3
|
UTSW |
1 |
82,650,400 (GRCm39) |
missense |
unknown |
|
|
R4928:Col4a3
|
UTSW |
1 |
82,688,698 (GRCm39) |
unclassified |
probably benign |
|
|
R5044:Col4a3
|
UTSW |
1 |
82,644,267 (GRCm39) |
missense |
unknown |
|
|
R5557:Col4a3
|
UTSW |
1 |
82,692,968 (GRCm39) |
unclassified |
probably benign |
|
|
R5761:Col4a3
|
UTSW |
1 |
82,693,778 (GRCm39) |
nonsense |
probably null |
|
|
R5970:Col4a3
|
UTSW |
1 |
82,694,050 (GRCm39) |
missense |
possibly damaging |
0.76 |
|
R6576:Col4a3
|
UTSW |
1 |
82,686,295 (GRCm39) |
splice site |
probably null |
|
|
R6583:Col4a3
|
UTSW |
1 |
82,619,197 (GRCm39) |
missense |
unknown |
|
|
R6675:Col4a3
|
UTSW |
1 |
82,646,646 (GRCm39) |
missense |
unknown |
|
|
R7170:Col4a3
|
UTSW |
1 |
82,693,630 (GRCm39) |
splice site |
probably null |
|
|
R7592:Col4a3
|
UTSW |
1 |
82,626,338 (GRCm39) |
missense |
unknown |
|
|
R7624:Col4a3
|
UTSW |
1 |
82,696,605 (GRCm39) |
missense |
probably benign |
|
|
R7994:Col4a3
|
UTSW |
1 |
82,640,627 (GRCm39) |
missense |
unknown |
|
|
R8127:Col4a3
|
UTSW |
1 |
82,627,481 (GRCm39) |
missense |
unknown |
|
|
R8702:Col4a3
|
UTSW |
1 |
82,688,700 (GRCm39) |
missense |
unknown |
|
|
R8865:Col4a3
|
UTSW |
1 |
82,647,483 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8973:Col4a3
|
UTSW |
1 |
82,693,052 (GRCm39) |
missense |
probably benign |
0.11 |
|
R9611:Col4a3
|
UTSW |
1 |
82,678,018 (GRCm39) |
missense |
unknown |
|
|
R9665:Col4a3
|
UTSW |
1 |
82,668,301 (GRCm39) |
missense |
unknown |
|
|
R9765:Col4a3
|
UTSW |
1 |
82,646,678 (GRCm39) |
nonsense |
probably null |
|
|
X0067:Col4a3
|
UTSW |
1 |
82,693,880 (GRCm39) |
missense |
probably damaging |
0.99 |
|
Z1177:Col4a3
|
UTSW |
1 |
82,667,760 (GRCm39) |
missense |
unknown |
|
|
| Predicted Primers |
PCR Primer
(F):5'- AGCCCACTCGTCTCTAAGATTC -3'
(R):5'- TTGTTTACAGTGACCTTCAGGG -3'
Sequencing Primer
(F):5'- TTTCATATTTGAGGCTTACCAGC -3'
(R):5'- TTCAGGGGAAGCTCGAATCC -3'
|
| Posted On |
2015-04-17 |
Incidental Mutation