Incidental Mutation 'R0319:Vcam1'
| ID |
25529 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vcam1
|
| Ensembl Gene |
ENSMUSG00000027962 |
| Gene Name |
vascular cell adhesion molecule 1 |
| Synonyms |
CD106, Vcam-1 |
| MMRRC Submission |
038529-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.554)
|
| Stock # |
R0319 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
115903669-115923337 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 115909709 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Methionine
at position 539
(I539M)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000029574
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029574]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029574
AA Change: I539M
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000029574
Gene: ENSMUSG00000027962
AA Change: I539M
| Domain | Start | End | E-Value | Type |
|---|
|
IG
|
32 |
113 |
2.41e-6 |
SMART |
|
Pfam:C2-set
|
133 |
221 |
4.5e-27 |
PFAM |
|
IGc2
|
237 |
298 |
2.09e-15 |
SMART |
|
IGc2
|
326 |
390 |
8.38e-6 |
SMART |
|
Pfam:C2-set
|
421 |
509 |
7.2e-26 |
PFAM |
|
IGc2
|
525 |
586 |
7.35e-11 |
SMART |
|
IG
|
608 |
686 |
2.25e-6 |
SMART |
|
transmembrane domain
|
699 |
721 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000197031
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 98.9%
- 3x: 97.8%
- 10x: 95.0%
- 20x: 89.1%
|
| Validation Efficiency |
100% (58/58) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the Ig superfamily and encodes a cell surface sialoglycoprotein expressed by cytokine-activated endothelium. This type I membrane protein mediates leukocyte-endothelial cell adhesion and signal transduction, and may play a role in the development of artherosclerosis and rheumatoid arthritis. Three alternatively spliced transcripts encoding different isoforms have been described for this gene. [provided by RefSeq, Dec 2010]
PHENOTYPE: Most homozygous null mutants die by embryonic day 12.5 due to defective placenta and failure of chorion/allantois fusion, and heart developmental anomalies. Survivors are generally normal, but have high numbers of circulating blood mononuclear leukocytes. [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 |
|---|
| 9130023H24Rik |
A |
C |
7: 127,836,362 (GRCm39) |
V77G |
probably benign |
Het |
| Abcb1b |
A |
G |
5: 8,877,428 (GRCm39) |
R663G |
probably benign |
Het |
| Acly |
A |
G |
11: 100,395,808 (GRCm39) |
V404A |
probably damaging |
Het |
| Actg2 |
T |
A |
6: 83,497,725 (GRCm39) |
I103F |
probably damaging |
Het |
| Anapc5 |
A |
G |
5: 122,956,919 (GRCm39) |
V120A |
probably damaging |
Het |
| Ankk1 |
T |
G |
9: 49,327,371 (GRCm39) |
T603P |
probably damaging |
Het |
| Ankmy2 |
T |
C |
12: 36,215,898 (GRCm39) |
S33P |
possibly damaging |
Het |
| Arhgef19 |
A |
T |
4: 140,983,710 (GRCm39) |
T748S |
possibly damaging |
Het |
| Atad5 |
T |
A |
11: 80,011,616 (GRCm39) |
|
probably benign |
Het |
| Atxn10 |
T |
C |
15: 85,249,483 (GRCm39) |
L105P |
probably damaging |
Het |
| Cacna1s |
T |
C |
1: 135,998,455 (GRCm39) |
V161A |
probably damaging |
Het |
| Col6a3 |
T |
C |
1: 90,735,426 (GRCm39) |
E741G |
possibly damaging |
Het |
| Cpne9 |
G |
A |
6: 113,271,654 (GRCm39) |
G338E |
probably damaging |
Het |
| Cyp3a13 |
G |
A |
5: 137,897,124 (GRCm39) |
P397S |
probably damaging |
Het |
| Dbn1 |
C |
T |
13: 55,622,729 (GRCm39) |
E585K |
probably damaging |
Het |
| Draxin |
A |
G |
4: 148,200,429 (GRCm39) |
L7P |
probably benign |
Het |
| Exosc7 |
T |
A |
9: 122,960,025 (GRCm39) |
|
probably benign |
Het |
| Far2 |
A |
G |
6: 148,058,968 (GRCm39) |
E218G |
probably damaging |
Het |
| Ggps1 |
A |
C |
13: 14,228,462 (GRCm39) |
N240K |
possibly damaging |
Het |
| Kcnip1 |
T |
C |
11: 33,601,529 (GRCm39) |
|
probably benign |
Het |
| Kcnv2 |
A |
T |
19: 27,301,424 (GRCm39) |
Y425F |
probably benign |
Het |
| Kdelr2 |
T |
A |
5: 143,398,272 (GRCm39) |
F40I |
probably damaging |
Het |
| Kdm1b |
C |
T |
13: 47,207,195 (GRCm39) |
P173L |
probably benign |
Het |
| Kif20b |
G |
A |
19: 34,925,132 (GRCm39) |
|
probably benign |
Het |
| Klhl9 |
A |
T |
4: 88,638,691 (GRCm39) |
Y517N |
possibly damaging |
Het |
| Lgals3bp |
A |
G |
11: 118,284,347 (GRCm39) |
S411P |
probably damaging |
Het |
| Lmo3 |
G |
A |
6: 138,354,309 (GRCm39) |
T85M |
probably damaging |
Het |
| Lvrn |
C |
A |
18: 46,997,820 (GRCm39) |
T256N |
probably damaging |
Het |
| Malt1 |
T |
C |
18: 65,595,986 (GRCm39) |
|
probably null |
Het |
| Mgst1 |
A |
G |
6: 138,133,155 (GRCm39) |
I157V |
possibly damaging |
Het |
| Mob3a |
A |
T |
10: 80,525,819 (GRCm39) |
V164E |
possibly damaging |
Het |
| Mprip |
T |
A |
11: 59,587,864 (GRCm39) |
|
probably benign |
Het |
| Mst1 |
A |
G |
9: 107,959,712 (GRCm39) |
N276S |
probably benign |
Het |
| Or5an1b |
A |
T |
19: 12,299,680 (GRCm39) |
C170* |
probably null |
Het |
| P3h2 |
T |
A |
16: 25,789,681 (GRCm39) |
I529F |
possibly damaging |
Het |
| Pikfyve |
T |
A |
1: 65,285,490 (GRCm39) |
S865T |
probably benign |
Het |
| Rcbtb2 |
G |
A |
14: 73,415,909 (GRCm39) |
R474Q |
probably benign |
Het |
| Rpl27 |
G |
A |
11: 101,334,321 (GRCm39) |
|
probably benign |
Het |
| Rtp1 |
G |
A |
16: 23,250,210 (GRCm39) |
E192K |
probably damaging |
Het |
| Sgk2 |
T |
C |
2: 162,837,592 (GRCm39) |
|
probably benign |
Het |
| Slc17a3 |
C |
T |
13: 24,039,841 (GRCm39) |
S293F |
probably damaging |
Het |
| Slc49a4 |
T |
C |
16: 35,570,884 (GRCm39) |
D140G |
probably benign |
Het |
| Spdl1 |
T |
C |
11: 34,714,347 (GRCm39) |
N114S |
possibly damaging |
Het |
| Syne2 |
C |
T |
12: 76,110,936 (GRCm39) |
R5756W |
probably damaging |
Het |
| Tor1aip1 |
T |
C |
1: 155,882,927 (GRCm39) |
E307G |
probably damaging |
Het |
| Tpd52 |
T |
C |
3: 9,018,749 (GRCm39) |
T44A |
probably benign |
Het |
| Trim67 |
A |
T |
8: 125,549,966 (GRCm39) |
Y532F |
probably damaging |
Het |
| Ttll9 |
C |
A |
2: 152,842,018 (GRCm39) |
|
probably null |
Het |
| Ush2a |
T |
C |
1: 188,680,571 (GRCm39) |
|
probably benign |
Het |
| Vmn1r19 |
T |
A |
6: 57,381,600 (GRCm39) |
M51K |
possibly damaging |
Het |
| Vmn2r61 |
T |
A |
7: 41,949,941 (GRCm39) |
M787K |
probably damaging |
Het |
| Xdh |
T |
A |
17: 74,213,096 (GRCm39) |
|
probably benign |
Het |
| Zfp109 |
A |
T |
7: 23,933,895 (GRCm39) |
V8E |
probably damaging |
Het |
| Zfp595 |
G |
A |
13: 67,464,577 (GRCm39) |
A562V |
possibly damaging |
Het |
| Zfp759 |
A |
G |
13: 67,288,356 (GRCm39) |
T636A |
probably benign |
Het |
|
| Other mutations in Vcam1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00717:Vcam1
|
APN |
3 |
115,908,120 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
IGL01546:Vcam1
|
APN |
3 |
115,909,591 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
IGL01548:Vcam1
|
APN |
3 |
115,909,600 (GRCm39) |
missense |
probably benign |
0.06 |
|
IGL02070:Vcam1
|
APN |
3 |
115,919,646 (GRCm39) |
missense |
probably benign |
0.07 |
|
IGL02353:Vcam1
|
APN |
3 |
115,909,543 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
IGL02360:Vcam1
|
APN |
3 |
115,909,543 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
K7371:Vcam1
|
UTSW |
3 |
115,918,298 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0310:Vcam1
|
UTSW |
3 |
115,908,065 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R0468:Vcam1
|
UTSW |
3 |
115,909,595 (GRCm39) |
nonsense |
probably null |
|
|
R0638:Vcam1
|
UTSW |
3 |
115,910,908 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R1070:Vcam1
|
UTSW |
3 |
115,904,552 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
R1728:Vcam1
|
UTSW |
3 |
115,908,164 (GRCm39) |
missense |
probably benign |
0.16 |
|
R1784:Vcam1
|
UTSW |
3 |
115,908,164 (GRCm39) |
missense |
probably benign |
0.16 |
|
R1956:Vcam1
|
UTSW |
3 |
115,919,606 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1957:Vcam1
|
UTSW |
3 |
115,919,606 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3052:Vcam1
|
UTSW |
3 |
115,918,079 (GRCm39) |
splice site |
probably null |
|
|
R3832:Vcam1
|
UTSW |
3 |
115,908,140 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R4297:Vcam1
|
UTSW |
3 |
115,910,892 (GRCm39) |
missense |
probably benign |
|
|
R4801:Vcam1
|
UTSW |
3 |
115,909,584 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4802:Vcam1
|
UTSW |
3 |
115,909,584 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4970:Vcam1
|
UTSW |
3 |
115,910,941 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5073:Vcam1
|
UTSW |
3 |
115,918,037 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5074:Vcam1
|
UTSW |
3 |
115,918,037 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5112:Vcam1
|
UTSW |
3 |
115,910,941 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5597:Vcam1
|
UTSW |
3 |
115,919,651 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6035:Vcam1
|
UTSW |
3 |
115,919,606 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6035:Vcam1
|
UTSW |
3 |
115,919,606 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6120:Vcam1
|
UTSW |
3 |
115,918,049 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6617:Vcam1
|
UTSW |
3 |
115,919,711 (GRCm39) |
missense |
possibly damaging |
0.48 |
|
R7232:Vcam1
|
UTSW |
3 |
115,919,628 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R7350:Vcam1
|
UTSW |
3 |
115,908,211 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7384:Vcam1
|
UTSW |
3 |
115,910,877 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R7571:Vcam1
|
UTSW |
3 |
115,908,032 (GRCm39) |
nonsense |
probably null |
|
|
R7606:Vcam1
|
UTSW |
3 |
115,914,704 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R7742:Vcam1
|
UTSW |
3 |
115,909,734 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R8151:Vcam1
|
UTSW |
3 |
115,918,128 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R8965:Vcam1
|
UTSW |
3 |
115,922,422 (GRCm39) |
nonsense |
probably null |
|
|
R8997:Vcam1
|
UTSW |
3 |
115,910,977 (GRCm39) |
missense |
probably benign |
|
|
R9182:Vcam1
|
UTSW |
3 |
115,911,004 (GRCm39) |
missense |
probably benign |
|
|
R9224:Vcam1
|
UTSW |
3 |
115,904,592 (GRCm39) |
nonsense |
probably null |
|
|
R9540:Vcam1
|
UTSW |
3 |
115,911,019 (GRCm39) |
missense |
possibly damaging |
0.78 |
|
R9725:Vcam1
|
UTSW |
3 |
115,922,287 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R9729:Vcam1
|
UTSW |
3 |
115,911,105 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Vcam1
|
UTSW |
3 |
115,922,990 (GRCm39) |
missense |
not run |
|
|
| Predicted Primers |
PCR Primer
(F):5'- ACATAAAGTCACACACTGCTTACCTTGG -3'
(R):5'- TGTCTCCCCTACAGAAACATCCTGG -3'
Sequencing Primer
(F):5'- CACACTGCTTACCTTGGATAATCAG -3'
(R):5'- AGAAACATCCTGGGCTGGTTATC -3'
|
| Posted On |
2013-04-16 |
Incidental Mutation