Incidental Mutation 'R1760:Vegfa'
ID 192736
Institutional Source Beutler Lab
Gene Symbol Vegfa
Ensembl Gene ENSMUSG00000023951
Gene Name vascular endothelial growth factor A
Synonyms VEGF-A, VEGF120, VEGF188, VEGF164, VPF, Vegf
MMRRC Submission 039792-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1760 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 46327919-46343295 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 46336395 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 242 (Y242H)
Ref Sequence ENSEMBL: ENSMUSP00000115883 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000024747] [ENSMUST00000071648] [ENSMUST00000113519] [ENSMUST00000113520] [ENSMUST00000142351] [ENSMUST00000167860] [ENSMUST00000217017] [ENSMUST00000214739]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000024747
AA Change: Y64H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000024747
Gene: ENSMUSG00000023951
AA Change: Y64H

DomainStartEndE-ValueType
PDGF 49 131 1.48e-49 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000071648
AA Change: Y242H

PolyPhen 2 Score 0.688 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000071575
Gene: ENSMUSG00000023951
AA Change: Y242H

DomainStartEndE-ValueType
low complexity region 31 51 N/A INTRINSIC
low complexity region 60 71 N/A INTRINSIC
low complexity region 87 105 N/A INTRINSIC
low complexity region 121 143 N/A INTRINSIC
low complexity region 158 176 N/A INTRINSIC
PDGF 227 309 1.48e-49 SMART
Pfam:VEGF_C 312 368 2.3e-35 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000113519
AA Change: Y64H

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000109147
Gene: ENSMUSG00000023951
AA Change: Y64H

DomainStartEndE-ValueType
PDGF 49 131 1.48e-49 SMART
low complexity region 140 161 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000113520
AA Change: Y64H

PolyPhen 2 Score 0.439 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000109148
Gene: ENSMUSG00000023951
AA Change: Y64H

DomainStartEndE-ValueType
PDGF 49 131 1.48e-49 SMART
Pfam:VEGF_C 154 208 9.5e-35 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133605
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142321
Predicted Effect probably damaging
Transcript: ENSMUST00000142351
AA Change: Y242H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000115883
Gene: ENSMUSG00000023951
AA Change: Y242H

DomainStartEndE-ValueType
low complexity region 31 51 N/A INTRINSIC
low complexity region 60 71 N/A INTRINSIC
low complexity region 87 105 N/A INTRINSIC
low complexity region 121 143 N/A INTRINSIC
low complexity region 158 176 N/A INTRINSIC
PDGF 227 309 1.48e-49 SMART
Pfam:VEGF_C 339 392 1.9e-31 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000167860
AA Change: Y242H

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000131901
Gene: ENSMUSG00000023951
AA Change: Y242H

DomainStartEndE-ValueType
low complexity region 31 51 N/A INTRINSIC
low complexity region 60 71 N/A INTRINSIC
low complexity region 87 105 N/A INTRINSIC
low complexity region 121 143 N/A INTRINSIC
low complexity region 158 176 N/A INTRINSIC
PDGF 227 309 1.48e-49 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143985
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146149
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150327
Predicted Effect probably damaging
Transcript: ENSMUST00000217017
AA Change: Y242H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
Predicted Effect possibly damaging
Transcript: ENSMUST00000214739
AA Change: Y242H

PolyPhen 2 Score 0.851 (Sensitivity: 0.83; Specificity: 0.93)
Meta Mutation Damage Score 0.4976 question?
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 96.9%
  • 10x: 95.3%
  • 20x: 92.6%
Validation Efficiency 97% (95/98)
MGI Phenotype FUNCTION: This gene is a member of the PDGF/VEGF growth factor family. It encodes a heparin-binding protein, which exists as a disulfide-linked homodimer. This growth factor induces proliferation and migration of vascular endothelial cells, and is essential for both physiological and pathological angiogenesis. Disruption of this gene in mice resulted in abnormal embryonic blood vessel formation. This gene is upregulated in many known tumors and its expression is correlated with tumor stage and progression. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. There is also evidence for alternative translation initiation from upstream non-AUG (CUG) codons resulting in additional isoforms. A recent study showed that a C-terminally extended isoform is produced by use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism, and that this isoform is antiangiogenic. Expression of some isoforms derived from the AUG start codon is regulated by a small upstream open reading frame, which is located within an internal ribosome entry site.[provided by RefSeq, Nov 2015]
PHENOTYPE: Hetero- or homozygous null mutants show embryonic lethality with impaired angiogenesis and blood-island formation. Mutants selectively expressing isoform 120 or 188 exhibit vascular outgrowth/patterning defects or impaired arterial development, respectively. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 92 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca2 T C 2: 25,333,055 (GRCm39) S1585P probably benign Het
Abhd16b T C 2: 181,135,197 (GRCm39) F33S probably damaging Het
Adgra2 G A 8: 27,609,795 (GRCm39) R856Q probably damaging Het
Aff3 A T 1: 38,368,945 (GRCm39) probably benign Het
Anxa2 A T 9: 69,397,049 (GRCm39) Y251F probably benign Het
Arid1b A G 17: 5,392,088 (GRCm39) T1873A probably damaging Het
Baz1b C A 5: 135,271,378 (GRCm39) D1320E probably benign Het
Bbs1 A T 19: 4,944,350 (GRCm39) S426R probably benign Het
Bid A G 6: 120,877,209 (GRCm39) V44A possibly damaging Het
Ccdc60 T A 5: 116,310,532 (GRCm39) M177L probably damaging Het
Cdh23 G A 10: 60,161,855 (GRCm39) T1997M probably damaging Het
Cdh5 T A 8: 104,854,801 (GRCm39) M243K probably benign Het
Clpb T A 7: 101,435,905 (GRCm39) V578E possibly damaging Het
Cngb1 C A 8: 96,026,328 (GRCm39) C151F probably benign Het
Cntnap5b T C 1: 99,700,535 (GRCm39) S16P probably benign Het
Cr1l T A 1: 194,797,123 (GRCm39) M305L probably benign Het
Ctnnal1 A T 4: 56,838,988 (GRCm39) M235K probably damaging Het
Ddx55 A T 5: 124,706,176 (GRCm39) R534W probably damaging Het
Dip2b T A 15: 100,109,910 (GRCm39) L1465Q probably damaging Het
Dnah9 G T 11: 65,872,048 (GRCm39) D2727E probably benign Het
Dph3b-ps A C 13: 106,683,497 (GRCm39) noncoding transcript Het
Dst T A 1: 34,267,684 (GRCm39) L2702Q probably damaging Het
Efnb2 T C 8: 8,673,184 (GRCm39) T158A possibly damaging Het
Exosc10 A T 4: 148,662,926 (GRCm39) K712* probably null Het
Fgr T C 4: 132,725,653 (GRCm39) V354A possibly damaging Het
Fsip2 A G 2: 82,830,185 (GRCm39) D6893G possibly damaging Het
Fsip2 G A 2: 82,815,240 (GRCm39) V3658M probably benign Het
Fsip2 A T 2: 82,818,055 (GRCm39) H4596L possibly damaging Het
Gm1527 G A 3: 28,949,699 (GRCm39) probably benign Het
Gm5150 G T 3: 16,060,468 (GRCm39) Q7K probably benign Het
Gpr155 C T 2: 73,212,279 (GRCm39) V115M probably damaging Het
Gpr75 T C 11: 30,841,527 (GRCm39) L144P probably damaging Het
Gsn T A 2: 35,174,835 (GRCm39) Y127N probably damaging Het
Hk1 A G 10: 62,117,678 (GRCm39) L615S probably damaging Het
Igsf9b A G 9: 27,229,123 (GRCm39) T194A possibly damaging Het
Il17rd C T 14: 26,813,763 (GRCm39) Q46* probably null Het
Jak1 T A 4: 101,020,126 (GRCm39) M678L probably benign Het
Kif6 T C 17: 49,922,311 (GRCm39) V16A probably benign Het
Kpna3 T C 14: 61,607,990 (GRCm39) E405G probably benign Het
Lmtk2 C A 5: 144,110,993 (GRCm39) T571K probably damaging Het
Mucl2 T C 15: 103,927,838 (GRCm39) T40A possibly damaging Het
Myh11 G A 16: 14,051,559 (GRCm39) probably benign Het
Myh7 C T 14: 55,210,170 (GRCm39) R1845Q probably damaging Het
Myo1f T A 17: 33,805,172 (GRCm39) L480Q probably benign Het
Nek9 T G 12: 85,352,364 (GRCm39) D833A possibly damaging Het
Nek9 T C 12: 85,357,184 (GRCm39) E660G probably benign Het
Or10z1 C T 1: 174,077,926 (GRCm39) C189Y probably damaging Het
Or2a12 A G 6: 42,904,431 (GRCm39) I89V possibly damaging Het
Or2t45 A G 11: 58,669,195 (GRCm39) M81V possibly damaging Het
Or5h18 T C 16: 58,847,350 (GRCm39) R307G probably benign Het
Or6c65 T A 10: 129,603,417 (GRCm39) D17E probably benign Het
Or6f2 G A 7: 139,756,188 (GRCm39) V52M probably damaging Het
Or7s1a-ps1 T A 9: 18,843,791 (GRCm39) probably benign Het
Otud3 G T 4: 138,623,092 (GRCm39) T383K possibly damaging Het
Pkp4 T C 2: 59,142,185 (GRCm39) L496P probably damaging Het
Pla2g4e C A 2: 120,000,527 (GRCm39) A737S possibly damaging Het
Pla2g4f T C 2: 120,144,547 (GRCm39) probably benign Het
Plxnd1 A T 6: 115,944,740 (GRCm39) V1018E possibly damaging Het
Ppp1r21 T G 17: 88,869,653 (GRCm39) V402G possibly damaging Het
Prkcq T G 2: 11,304,881 (GRCm39) M690R probably damaging Het
Ptpra T C 2: 130,391,747 (GRCm39) I719T probably damaging Het
Rab3ip C T 10: 116,773,415 (GRCm39) D133N probably damaging Het
Relch T G 1: 105,647,169 (GRCm39) probably benign Het
Rsbn1 T A 3: 103,867,347 (GRCm39) Y563N probably damaging Het
Rtf1 A C 2: 119,558,889 (GRCm39) D530A probably benign Het
Rybp G T 6: 100,209,224 (GRCm39) S199R probably benign Het
Sema5a T G 15: 32,641,252 (GRCm39) C689G probably damaging Het
Senp6 T A 9: 80,025,911 (GRCm39) V314E probably benign Het
Setd1a T A 7: 127,385,062 (GRCm39) C47S possibly damaging Het
Slamf1 C A 1: 171,604,734 (GRCm39) T168K probably benign Het
Slc12a5 T C 2: 164,838,048 (GRCm39) S937P probably damaging Het
Slc38a11 C T 2: 65,185,663 (GRCm39) probably null Het
Slc6a2 C T 8: 93,687,846 (GRCm39) probably benign Het
Snw1 A T 12: 87,511,459 (GRCm39) F64Y probably benign Het
Spata9 A C 13: 76,146,643 (GRCm39) I172L probably benign Het
Sphkap T C 1: 83,255,265 (GRCm39) H828R probably benign Het
Spmip6 T A 4: 41,507,330 (GRCm39) probably null Het
Tmem94 A T 11: 115,687,580 (GRCm39) K1146N probably damaging Het
Trdn A G 10: 33,109,883 (GRCm39) T294A possibly damaging Het
Tsc22d1 T C 14: 76,654,388 (GRCm39) V289A possibly damaging Het
Tti1 C A 2: 157,834,955 (GRCm39) V1002L possibly damaging Het
Tubgcp4 T A 2: 121,019,952 (GRCm39) probably null Het
Ush2a G A 1: 188,643,180 (GRCm39) E4181K possibly damaging Het
Uvrag A G 7: 98,537,555 (GRCm39) S547P probably benign Het
Vav3 T C 3: 109,248,443 (GRCm39) V30A possibly damaging Het
Vmn2r75 G T 7: 85,798,019 (GRCm39) T598K probably damaging Het
Vps13b C T 15: 35,884,765 (GRCm39) S3146L possibly damaging Het
Vrk3 A G 7: 44,417,895 (GRCm39) Y310C probably damaging Het
Zfhx4 A G 3: 5,447,676 (GRCm39) K1100R probably benign Het
Zfp748 T A 13: 67,693,540 (GRCm39) probably null Het
Zfp760 A T 17: 21,941,311 (GRCm39) D162V probably damaging Het
Znfx1 T A 2: 166,881,786 (GRCm39) M1068L probably damaging Het
Other mutations in Vegfa
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01355:Vegfa APN 17 46,336,347 (GRCm39) missense possibly damaging 0.88
IGL02859:Vegfa APN 17 46,335,421 (GRCm39) missense probably benign 0.43
R1442:Vegfa UTSW 17 46,336,418 (GRCm39) missense possibly damaging 0.85
R1982:Vegfa UTSW 17 46,329,786 (GRCm39) makesense probably null
R2012:Vegfa UTSW 17 46,336,284 (GRCm39) missense probably benign 0.21
R3729:Vegfa UTSW 17 46,335,446 (GRCm39) missense possibly damaging 0.80
R4276:Vegfa UTSW 17 46,342,392 (GRCm39) missense probably benign
R4277:Vegfa UTSW 17 46,342,392 (GRCm39) missense probably benign
R4279:Vegfa UTSW 17 46,342,392 (GRCm39) missense probably benign
R4654:Vegfa UTSW 17 46,336,176 (GRCm39) intron probably benign
R4696:Vegfa UTSW 17 46,339,272 (GRCm39) splice site probably null
R7798:Vegfa UTSW 17 46,342,761 (GRCm39) missense probably damaging 1.00
R7863:Vegfa UTSW 17 46,336,461 (GRCm39) missense probably damaging 1.00
R7946:Vegfa UTSW 17 46,336,377 (GRCm39) missense probably damaging 0.96
R8235:Vegfa UTSW 17 46,342,236 (GRCm39) missense possibly damaging 0.91
R8683:Vegfa UTSW 17 46,342,396 (GRCm39) missense probably benign 0.35
R8756:Vegfa UTSW 17 46,342,465 (GRCm39) missense probably damaging 1.00
R9700:Vegfa UTSW 17 46,342,713 (GRCm39) missense probably damaging 1.00
R9701:Vegfa UTSW 17 46,342,713 (GRCm39) missense probably damaging 1.00
R9733:Vegfa UTSW 17 46,335,401 (GRCm39) missense probably damaging 1.00
X0026:Vegfa UTSW 17 46,336,452 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GAGGCCCAGACAACCTTCTAATGC -3'
(R):5'- TGTACCCAGACTCAGGCTGTCATC -3'

Sequencing Primer
(F):5'- GACAACCTTCTAATGCCCCTC -3'
(R):5'- ACTCAGGCTGTCATCTGGAG -3'
Posted On 2014-05-23