Incidental Mutation 'R7946:Vegfa'
ID 649375
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 045991-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7946 (G1)
Quality Score 225.009
Status Validated
Chromosome 17
Chromosomal Location 46327919-46343295 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 46336377 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Asparagine at position 248 (Y248N)
Ref Sequence ENSEMBL: ENSMUSP00000115883 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000024747] [ENSMUST00000071648] [ENSMUST00000113519] [ENSMUST00000113520] [ENSMUST00000142351] [ENSMUST00000167860] [ENSMUST00000214739] [ENSMUST00000217017]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000024747
AA Change: Y70N

PolyPhen 2 Score 0.955 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000024747
Gene: ENSMUSG00000023951
AA Change: Y70N

DomainStartEndE-ValueType
PDGF 49 131 1.48e-49 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000071648
AA Change: Y248N

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000071575
Gene: ENSMUSG00000023951
AA Change: Y248N

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: Y70N

PolyPhen 2 Score 0.885 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000109147
Gene: ENSMUSG00000023951
AA Change: Y70N

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: Y70N

PolyPhen 2 Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000109148
Gene: ENSMUSG00000023951
AA Change: Y70N

DomainStartEndE-ValueType
PDGF 49 131 1.48e-49 SMART
Pfam:VEGF_C 154 208 9.5e-35 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000142351
AA Change: Y248N

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000115883
Gene: ENSMUSG00000023951
AA Change: Y248N

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 possibly damaging
Transcript: ENSMUST00000167860
AA Change: Y248N

PolyPhen 2 Score 0.955 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000131901
Gene: ENSMUSG00000023951
AA Change: Y248N

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 probably damaging
Transcript: ENSMUST00000214739
AA Change: Y248N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
Predicted Effect possibly damaging
Transcript: ENSMUST00000217017
AA Change: Y248N

PolyPhen 2 Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)
Meta Mutation Damage Score 0.1452 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.8%
Validation Efficiency 98% (54/55)
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca16 A G 7: 120,126,398 (GRCm39) T1186A probably benign Het
Adprhl1 C T 8: 13,298,682 (GRCm39) V83I probably damaging Het
Afap1 A G 5: 36,092,995 (GRCm39) N33S probably benign Het
Afap1 G A 5: 36,141,396 (GRCm39) probably null Het
Ampd3 A G 7: 110,377,147 (GRCm39) D46G probably damaging Het
Anks4b A G 7: 119,781,707 (GRCm39) K246R probably benign Het
Aqp9 C T 9: 71,030,290 (GRCm39) V192M probably damaging Het
Aspscr1 T G 11: 120,599,443 (GRCm39) S132A Het
Atp2b4 C A 1: 133,658,320 (GRCm39) R530L probably damaging Het
Bahcc1 T C 11: 120,163,325 (GRCm39) V541A probably benign Het
Caprin1 A T 2: 103,603,093 (GRCm39) V490E probably damaging Het
Ccdc7a T A 8: 129,643,627 (GRCm39) K734M probably damaging Het
Ccdc9b G T 2: 118,590,146 (GRCm39) P233T probably benign Het
Cdc16 A G 8: 13,812,882 (GRCm39) K138R probably benign Het
Cela2a A G 4: 141,549,617 (GRCm39) S53P possibly damaging Het
Clca3a2 A G 3: 144,513,075 (GRCm39) probably null Het
Cntrob T C 11: 69,206,047 (GRCm39) E373G possibly damaging Het
Csmd2 T C 4: 128,414,058 (GRCm39) Y2633H Het
Ctbp1 A T 5: 33,407,688 (GRCm39) M296K probably benign Het
Dido1 G T 2: 180,303,501 (GRCm39) Q1468K possibly damaging Het
Dnah7b T C 1: 46,272,739 (GRCm39) F2289S probably damaging Het
Fndc7 T A 3: 108,779,452 (GRCm39) D364V possibly damaging Het
Ggt7 G T 2: 155,347,892 (GRCm39) H180Q probably damaging Het
Gm14399 A T 2: 174,973,273 (GRCm39) C161S probably damaging Het
Gm17324 T C 9: 78,355,794 (GRCm39) T62A unknown Het
Gpr107 A G 2: 31,078,716 (GRCm39) I384V probably damaging Het
Igsf10 C A 3: 59,227,125 (GRCm39) V2183L possibly damaging Het
Il23r T A 6: 67,411,648 (GRCm39) H363L possibly damaging Het
Inka2 T A 3: 105,623,761 (GRCm39) L45H probably damaging Het
Iqsec1 A T 6: 90,667,252 (GRCm39) I291N probably damaging Het
Kcnc3 A T 7: 44,245,569 (GRCm39) T620S probably benign Het
Kif2b T C 11: 91,466,571 (GRCm39) N571D probably benign Het
Klrb1c T A 6: 128,766,072 (GRCm39) probably benign Het
Mgst2 A G 3: 51,584,991 (GRCm39) N55S probably damaging Het
Neb T C 2: 52,102,746 (GRCm39) D4509G probably damaging Het
Obox1 G T 7: 15,289,456 (GRCm39) V82F probably benign Het
Or4k51 A T 2: 111,585,163 (GRCm39) M190L probably benign Het
Or5p59 A G 7: 107,703,053 (GRCm39) D179G probably benign Het
Or7e174 T C 9: 20,012,780 (GRCm39) S242P probably damaging Het
Pakap A T 4: 57,710,045 (GRCm39) N330I probably damaging Het
Phf21a A T 2: 92,189,512 (GRCm39) E590D probably damaging Het
Rai14 T C 15: 10,574,287 (GRCm39) probably null Het
Rfx7 T C 9: 72,524,096 (GRCm39) Y429H probably damaging Het
Spata31d1d G T 13: 59,878,606 (GRCm39) A77E probably benign Het
Stra8 A G 6: 34,907,816 (GRCm39) probably null Het
Syne1 A G 10: 5,200,919 (GRCm39) S3550P possibly damaging Het
Tars2 A T 3: 95,657,693 (GRCm39) H249Q probably damaging Het
Tomm5 T C 4: 45,107,969 (GRCm39) E22G probably benign Het
Tor1a A G 2: 30,853,704 (GRCm39) probably null Het
Trim43b A G 9: 88,973,538 (GRCm39) I65T probably damaging Het
Ubr3 T C 2: 69,781,739 (GRCm39) M640T possibly damaging Het
Vmn1r172 T G 7: 23,358,857 (GRCm39) probably null Het
Vmn1r29 G T 6: 58,284,834 (GRCm39) V185F probably benign Het
Wdfy4 G A 14: 32,826,072 (GRCm39) P1193L Het
Wdfy4 T C 14: 32,792,705 (GRCm39) K2114E 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
R1760:Vegfa UTSW 17 46,336,395 (GRCm39) missense probably damaging 1.00
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
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'- TACCAAAAGTTTCCCAGGCAG -3'
(R):5'- AAACACTTGTTTGGTGTGGAGC -3'

Sequencing Primer
(F):5'- GAGGCCCAGACAACCTTCTAATG -3'
(R):5'- CTGTAAGGAGTGGTCTCACAAATCTG -3'
Posted On 2020-09-15