Incidental Mutation 'R5073:Vcam1'
ID 388951
Institutional Source Beutler Lab
Gene Symbol Vcam1
Ensembl Gene ENSMUSG00000027962
Gene Name vascular cell adhesion molecule 1
Synonyms CD106, Vcam-1
MMRRC Submission 042662-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.554) question?
Stock # R5073 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 115903669-115923337 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 115918037 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 308 (V308A)
Ref Sequence ENSEMBL: ENSMUSP00000142876 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029574] [ENSMUST00000196309] [ENSMUST00000196449]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000029574
AA Change: V308A

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000029574
Gene: ENSMUSG00000027962
AA Change: V308A

DomainStartEndE-ValueType
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 probably benign
Transcript: ENSMUST00000196309
SMART Domains Protein: ENSMUSP00000143260
Gene: ENSMUSG00000027962

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
IG 38 119 1e-8 SMART
Pfam:C2-set 139 227 1.4e-25 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000196449
AA Change: V308A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000142876
Gene: ENSMUSG00000027962
AA Change: V308A

DomainStartEndE-ValueType
IG 32 113 2.41e-6 SMART
Pfam:C2-set 133 221 1.3e-27 PFAM
IGc2 237 298 2.09e-15 SMART
transmembrane domain 322 344 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197031
Predicted Effect noncoding transcript
Transcript: ENSMUST00000198269
Meta Mutation Damage Score 0.7669 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 92.6%
Validation Efficiency 100% (113/113)
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: 104 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca3 C T 17: 24,593,274 (GRCm39) R224C probably damaging Het
Adcy8 A T 15: 64,659,207 (GRCm39) W528R probably damaging Het
Agbl5 G A 5: 31,060,403 (GRCm39) R141Q probably damaging Het
Ahnak T A 19: 8,980,595 (GRCm39) H626Q probably benign Het
Ampd2 A T 3: 107,986,549 (GRCm39) M245K probably damaging Het
Apob G A 12: 8,055,219 (GRCm39) probably null Het
Apool C T X: 111,259,540 (GRCm39) Q60* probably null Het
Aqp1 A T 6: 55,322,520 (GRCm39) I172F probably damaging Het
Atp7a A G X: 105,153,374 (GRCm39) D1092G probably benign Het
Bcas3 A G 11: 85,261,958 (GRCm39) Y110C probably damaging Het
Brpf1 T C 6: 113,287,215 (GRCm39) S148P probably damaging Het
Capn3 A G 2: 120,322,301 (GRCm39) H339R probably damaging Het
Ccdc141 A T 2: 76,954,722 (GRCm39) probably null Het
Ccl2 A G 11: 81,927,984 (GRCm39) probably benign Het
Cct8l1 G A 5: 25,721,881 (GRCm39) V199I probably benign Het
Cdc23 C A 18: 34,784,742 (GRCm39) V7L unknown Het
Cit T A 5: 116,084,902 (GRCm39) M811K probably benign Het
Crim1 T C 17: 78,588,776 (GRCm39) C284R possibly damaging Het
Cyp2d10 C T 15: 82,287,954 (GRCm39) R383H probably benign Het
Cyp4a29 A G 4: 115,104,860 (GRCm39) T123A probably benign Het
Dbndd2 A G 2: 164,332,224 (GRCm39) probably benign Het
Dnaja3 A T 16: 4,514,289 (GRCm39) T274S probably damaging Het
Dot1l A G 10: 80,620,480 (GRCm39) D514G possibly damaging Het
Dysf A T 6: 84,114,254 (GRCm39) K1226M probably damaging Het
Eef1akmt1 A G 14: 57,803,464 (GRCm39) L30P probably damaging Het
Elavl1 A G 8: 4,351,741 (GRCm39) M125T possibly damaging Het
Eml4 C A 17: 83,771,006 (GRCm39) S723R probably damaging Het
Fgf15 A C 7: 144,450,576 (GRCm39) Y54S possibly damaging Het
Fign A T 2: 63,810,037 (GRCm39) L411* probably null Het
Flt1 C A 5: 147,620,749 (GRCm39) A132S probably benign Het
Fryl G A 5: 73,232,110 (GRCm39) P1550L probably damaging Het
Gas2l3 CACTCGTCATACT CACT 10: 89,266,820 (GRCm39) probably benign Het
Gprasp2 C T X: 134,743,346 (GRCm39) T235I possibly damaging Het
H2ab3 T C X: 119,222,543 (GRCm39) T84A probably damaging Het
Hal A T 10: 93,349,904 (GRCm39) I555F probably damaging Het
Hdac6 A G X: 7,811,036 (GRCm39) F104L probably damaging Het
Hibadh C T 6: 52,597,079 (GRCm39) V122M possibly damaging Het
Hmga1b C T 11: 120,654,012 (GRCm39) Q100* probably null Het
Hydin A G 8: 111,265,105 (GRCm39) N2763D probably benign Het
Ifi47 A G 11: 48,986,361 (GRCm39) T43A probably benign Het
Ifnlr1 A G 4: 135,432,457 (GRCm39) T298A probably benign Het
Impdh2 G A 9: 108,440,535 (GRCm39) probably null Het
Insr A G 8: 3,209,475 (GRCm39) F1203L probably damaging Het
Kcnq4 A G 4: 120,574,714 (GRCm39) S117P probably damaging Het
Kif19a G A 11: 114,658,053 (GRCm39) M37I probably benign Het
Kif1a T C 1: 92,950,227 (GRCm39) H1400R probably damaging Het
Kiss1r C A 10: 79,754,596 (GRCm39) S30* probably null Het
Krt222 T A 11: 99,134,796 (GRCm39) probably benign Het
Lekr1 A T 3: 65,727,215 (GRCm39) noncoding transcript Het
Ltn1 A G 16: 87,224,628 (GRCm39) V32A probably damaging Het
Marchf1 T A 8: 66,839,020 (GRCm39) W21R probably benign Het
Marchf5 A G 19: 37,188,207 (GRCm39) N58S possibly damaging Het
Mast4 G A 13: 102,875,391 (GRCm39) Q1158* probably null Het
Mib2 C G 4: 155,741,233 (GRCm39) A535P probably damaging Het
Mrtfa A G 15: 80,906,627 (GRCm39) V91A probably damaging Het
Msc C T 1: 14,824,537 (GRCm39) V178M probably benign Het
Muc4 C A 16: 32,754,529 (GRCm38) H1468N probably benign Het
Muc5b A T 7: 141,412,999 (GRCm39) T1982S unknown Het
Mvk A T 5: 114,591,013 (GRCm39) probably benign Het
Myo1a T C 10: 127,543,288 (GRCm39) probably null Het
Myo6 T G 9: 80,195,290 (GRCm39) S887A probably benign Het
Myo7a G A 7: 97,722,425 (GRCm39) Q1167* probably null Het
Ncald A T 15: 37,397,478 (GRCm39) H67Q probably damaging Het
Nmnat1 C A 4: 149,553,595 (GRCm39) M172I probably benign Het
Nudt1 G T 5: 140,317,662 (GRCm39) probably null Het
Nudt5 T A 2: 5,869,198 (GRCm39) H141Q probably benign Het
Or1m1 T C 9: 18,666,118 (GRCm39) E271G possibly damaging Het
Or4e1 T A 14: 52,701,032 (GRCm39) M118L probably damaging Het
Or8h10 A T 2: 86,808,666 (GRCm39) V158D possibly damaging Het
Parp14 A T 16: 35,655,077 (GRCm39) I1798K probably damaging Het
Pcdhga7 A G 18: 37,849,025 (GRCm39) D344G probably damaging Het
Pck1 A G 2: 172,998,770 (GRCm39) T343A probably benign Het
Pik3c2g T A 6: 139,665,873 (GRCm39) C65S probably null Het
Pilra A G 5: 137,833,674 (GRCm39) F131L probably damaging Het
Ppl A T 16: 4,906,742 (GRCm39) S1184R probably benign Het
Prmt2 C T 10: 76,058,390 (GRCm39) V140I probably damaging Het
Prpf38b A G 3: 108,818,484 (GRCm39) F92S probably damaging Het
Psmc3 A G 2: 90,884,915 (GRCm39) probably benign Het
Ptgs1 A T 2: 36,141,272 (GRCm39) N573I probably damaging Het
Rgs9 C A 11: 109,118,157 (GRCm39) A332S probably benign Het
Rptor T C 11: 119,787,305 (GRCm39) I1290T possibly damaging Het
Slc38a7 C A 8: 96,568,278 (GRCm39) R369L probably damaging Het
Slc4a2 G A 5: 24,643,760 (GRCm39) S855N probably benign Het
Slco2a1 G T 9: 102,923,925 (GRCm39) L46F probably damaging Het
Snrpd3 G T 10: 75,355,227 (GRCm39) C20F possibly damaging Het
Stab2 A T 10: 86,699,422 (GRCm39) I481N probably benign Het
Tbc1d9 A G 8: 83,960,176 (GRCm39) E143G probably damaging Het
Tenm2 T A 11: 35,959,208 (GRCm39) T1114S probably damaging Het
Tg A C 15: 66,607,101 (GRCm39) M213L probably benign Het
Tnc A G 4: 63,938,648 (GRCm39) C64R probably damaging Het
Tpd52l1 A G 10: 31,233,916 (GRCm39) L79S probably damaging Het
Tpp2 C A 1: 43,993,896 (GRCm39) S260R possibly damaging Het
Tppp2 G A 14: 52,157,912 (GRCm39) R119Q probably benign Het
Tshz2 A T 2: 169,804,493 (GRCm39) probably benign Het
Tuba8 T C 6: 121,199,862 (GRCm39) V182A probably damaging Het
Ufl1 A G 4: 25,254,780 (GRCm39) Y559H probably benign Het
Usp53 A T 3: 122,727,595 (GRCm39) S996T probably benign Het
Wdr17 T A 8: 55,143,271 (GRCm39) probably null Het
Wdr6 G A 9: 108,451,565 (GRCm39) H773Y probably damaging Het
Wnk4 T G 11: 101,152,014 (GRCm39) F173V probably damaging Het
Xrcc5 T C 1: 72,378,188 (GRCm39) Y395H probably damaging Het
Zcwpw1 T A 5: 137,793,781 (GRCm39) M1K probably null Het
Zfp263 A G 16: 3,564,704 (GRCm39) R240G possibly damaging Het
Zfp652 A G 11: 95,640,890 (GRCm39) I272V possibly damaging Het
Other mutations in Vcam1
AlleleSourceChrCoordTypePredicted EffectPPH 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
R0319:Vcam1 UTSW 3 115,909,709 (GRCm39) missense probably benign 0.01
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
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'- AATGCCAGTATCCACAGGGC -3'
(R):5'- CAGCTCCTGAGATTTTCTGGG -3'

Sequencing Primer
(F):5'- CCAGTATCCACAGGGCAGGAG -3'
(R):5'- TTCTGGGGCAGGAAGTTAGATAATG -3'
Posted On 2016-06-06