Incidental Mutation 'R5605:Gdpd4'
ID439245
Institutional Source Beutler Lab
Gene Symbol Gdpd4
Ensembl Gene ENSMUSG00000035582
Gene Nameglycerophosphodiester phosphodiesterase domain containing 4
Synonyms
MMRRC Submission 043270-MU
Accession Numbers
Is this an essential gene? Probably non essential (E-score: 0.081) question?
Stock #R5605 (G1)
Quality Score225
Status Validated
Chromosome7
Chromosomal Location97919955-98049663 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 98006300 bp
ZygosityHeterozygous
Amino Acid Change Valine to Alanine at position 562 (V562A)
Ref Sequence ENSEMBL: ENSMUSP00000131960 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041860] [ENSMUST00000170049]
Predicted Effect probably benign
Transcript: ENSMUST00000041860
AA Change: V562A

PolyPhen 2 Score 0.415 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000036772
Gene: ENSMUSG00000035582
AA Change: V562A

DomainStartEndE-ValueType
transmembrane domain 65 84 N/A INTRINSIC
transmembrane domain 104 135 N/A INTRINSIC
transmembrane domain 148 168 N/A INTRINSIC
transmembrane domain 183 205 N/A INTRINSIC
transmembrane domain 241 263 N/A INTRINSIC
Pfam:GDPD 281 440 1.4e-19 PFAM
transmembrane domain 543 565 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000170049
AA Change: V562A

PolyPhen 2 Score 0.415 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000131960
Gene: ENSMUSG00000035582
AA Change: V562A

DomainStartEndE-ValueType
transmembrane domain 65 84 N/A INTRINSIC
transmembrane domain 104 135 N/A INTRINSIC
transmembrane domain 148 168 N/A INTRINSIC
transmembrane domain 183 205 N/A INTRINSIC
transmembrane domain 241 263 N/A INTRINSIC
Pfam:GDPD 281 439 3.4e-21 PFAM
transmembrane domain 543 565 N/A INTRINSIC
Meta Mutation Damage Score 0.1128 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.5%
  • 20x: 95.9%
Validation Efficiency 100% (55/55)
Allele List at MGI
Other mutations in this stock
Total: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Afg3l2 C A 18: 67,442,355 G83* probably null Het
Arap2 A T 5: 62,615,067 M1476K possibly damaging Het
Catsper2 G A 2: 121,397,052 R546C possibly damaging Het
Ccdc109b T C 3: 129,917,009 E258G probably damaging Het
Ceacam5 T C 7: 17,747,236 F303L probably benign Het
Clvs1 A G 4: 9,281,751 D65G probably damaging Het
Coq5 T C 5: 115,283,717 probably null Het
D630045J12Rik A T 6: 38,191,764 V950E probably damaging Het
Dennd4b G A 3: 90,268,368 R148Q probably damaging Het
Dnah7c A G 1: 46,798,235 D3936G possibly damaging Het
Doc2b T C 11: 75,771,960 E404G probably damaging Het
Dsg1b C T 18: 20,399,539 P547S probably benign Het
Erich6 A G 3: 58,625,119 Y356H probably damaging Het
Galnt6 C T 15: 100,697,225 R465Q probably damaging Het
Gbp5 T C 3: 142,501,276 S69P probably damaging Het
Gm2075 T A 12: 88,011,998 C51S probably damaging Het
Gm340 T A 19: 41,582,863 I165N probably damaging Het
Greb1 A T 12: 16,708,726 V663D probably damaging Het
Gtf3c3 A T 1: 54,415,926 S593T probably benign Het
H2-Eb1 T C 17: 34,309,833 S113P probably benign Het
Herc3 C T 6: 58,857,727 R240C probably damaging Het
Iqub T C 6: 24,505,621 D96G probably benign Het
Kcnt2 A T 1: 140,574,743 E858D possibly damaging Het
Lrp2 C T 2: 69,523,299 R539K probably damaging Het
Lrrc10 C A 10: 117,045,900 P160T probably damaging Het
Map3k12 G T 15: 102,503,865 D280E probably benign Het
Mdn1 T C 4: 32,765,664 S5208P probably benign Het
Med20 C A 17: 47,623,144 probably benign Het
Mertk T C 2: 128,738,307 V227A probably benign Het
Mrvi1 C T 7: 110,946,002 C29Y possibly damaging Het
Ncstn A G 1: 172,081,150 probably benign Het
Nedd4l T C 18: 65,174,244 probably null Het
Nfyc A G 4: 120,790,489 probably benign Het
Npdc1 G A 2: 25,408,945 D284N probably damaging Het
Nt5dc1 C T 10: 34,403,695 C117Y probably benign Het
Nup88 A T 11: 70,944,070 probably benign Het
Olfr5 C T 7: 6,480,326 V277M probably benign Het
Pbrm1 T A 14: 31,035,992 I193K probably benign Het
Pcsk2 T C 2: 143,749,245 probably benign Het
Pdzd2 A T 15: 12,592,350 C69* probably null Het
Polr1e A G 4: 45,018,723 T18A probably benign Het
Prima1 T A 12: 103,199,904 I124F probably benign Het
Rbm34 T C 8: 126,949,419 K382R probably benign Het
Rftn1 T G 17: 50,047,407 N309T probably damaging Het
Sept1 C T 7: 127,215,426 D260N probably damaging Het
Serpina3g T C 12: 104,241,040 V154A probably damaging Het
Spef2 A T 15: 9,609,520 N1306K probably damaging Het
Stk4 T C 2: 164,079,566 F29S probably damaging Het
Stxbp5 A G 10: 9,769,746 probably benign Het
Tbl3 T C 17: 24,700,759 T774A probably benign Het
Tinag A G 9: 77,045,412 Y97H probably damaging Het
Tpm1 T C 9: 67,049,035 E33G probably damaging Het
Usp17lb T C 7: 104,840,640 E359G probably benign Het
Vmn2r91 A G 17: 18,136,501 E810G probably damaging Het
Vwce A T 19: 10,658,038 T633S possibly damaging Het
Ylpm1 G A 12: 85,028,853 R326H probably damaging Het
Other mutations in Gdpd4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00517:Gdpd4 APN 7 98004271 missense probably damaging 1.00
IGL01292:Gdpd4 APN 7 98014954 splice site probably benign
IGL01317:Gdpd4 APN 7 97998258 missense possibly damaging 0.74
IGL02678:Gdpd4 APN 7 97974377 splice site probably benign
IGL02822:Gdpd4 APN 7 97971924 missense possibly damaging 0.82
IGL02987:Gdpd4 APN 7 97961551 splice site probably benign
R0022:Gdpd4 UTSW 7 97982875 missense probably damaging 1.00
R0331:Gdpd4 UTSW 7 97973008 missense probably benign 0.11
R0882:Gdpd4 UTSW 7 97966298 missense probably damaging 1.00
R1425:Gdpd4 UTSW 7 97974012 missense probably benign 0.03
R1469:Gdpd4 UTSW 7 97974466 splice site probably null
R1469:Gdpd4 UTSW 7 97974466 splice site probably null
R1870:Gdpd4 UTSW 7 97972955 missense probably benign 0.00
R4747:Gdpd4 UTSW 7 97961633 missense possibly damaging 0.80
R5017:Gdpd4 UTSW 7 98004275 nonsense probably null
R5208:Gdpd4 UTSW 7 98014911 missense probably benign 0.11
R5290:Gdpd4 UTSW 7 97966336 missense possibly damaging 0.94
R5398:Gdpd4 UTSW 7 97971978 missense probably benign 0.00
R5715:Gdpd4 UTSW 7 97961597 missense probably benign 0.00
R5990:Gdpd4 UTSW 7 98040930 missense probably benign 0.00
R6269:Gdpd4 UTSW 7 97974462 missense probably damaging 1.00
R6314:Gdpd4 UTSW 7 97973953 missense probably damaging 0.98
R6817:Gdpd4 UTSW 7 97957830 missense probably benign 0.00
R6884:Gdpd4 UTSW 7 97972175 missense probably damaging 1.00
R7054:Gdpd4 UTSW 7 97973929 missense probably damaging 0.99
Z1088:Gdpd4 UTSW 7 97966309 missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- CCCAGTATGTATGCGGATGACT -3'
(R):5'- TGAGGGAGTAAGCTGCAGGC -3'

Sequencing Primer
(F):5'- AATAGCTGCAGGTAGTCTCACCTG -3'
(R):5'- CAGAAGGAAATGAGAGGCTGATATTC -3'
Posted On2016-10-26