Incidental Mutation 'IGL02934:Spdya'
ID 364241
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Spdya
Ensembl Gene ENSMUSG00000052525
Gene Name speedy/RINGO cell cycle regulator family, member A
Synonyms speedy A1, speedy/ringo, Spdy1, 4921517J08Rik, 4930548B21Rik, speedy A2
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.377) question?
Stock # IGL02934
Quality Score
Status
Chromosome 17
Chromosomal Location 71859056-71896528 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 71863395 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Isoleucine at position 48 (N48I)
Ref Sequence ENSEMBL: ENSMUSP00000063214 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000064420] [ENSMUST00000124001] [ENSMUST00000144142] [ENSMUST00000167641]
AlphaFold Q5IBH7
Predicted Effect probably benign
Transcript: ENSMUST00000064420
AA Change: N48I

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000063214
Gene: ENSMUSG00000052525
AA Change: N48I

DomainStartEndE-ValueType
Pfam:Spy1 68 198 8.2e-63 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000124001
AA Change: N48I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000118426
Gene: ENSMUSG00000052525
AA Change: N48I

DomainStartEndE-ValueType
Pfam:Spy1 68 198 1.5e-69 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130218
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130952
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137830
Predicted Effect probably benign
Transcript: ENSMUST00000144142
AA Change: N48I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000118994
Gene: ENSMUSG00000052525
AA Change: N48I

DomainStartEndE-ValueType
Pfam:Spy1 68 198 2.2e-62 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000167641
AA Change: N48I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000125912
Gene: ENSMUSG00000052525
AA Change: N48I

DomainStartEndE-ValueType
Pfam:Spy1 68 198 5.1e-69 PFAM
Coding Region Coverage
Validation Efficiency
MGI Phenotype PHENOTYPE: Homozygous inactivation of this gene results in impaired telomere attachment to the nuclear envelope during early meiosis, abnormal chromosome pairing and homologous synapsis, and meiotic prophase I arrest in male and female germ cells leading to infertility in both sexes. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca4 A T 3: 121,956,008 (GRCm39) R716* probably null Het
Abca8a A T 11: 109,931,414 (GRCm39) N1246K probably damaging Het
Acadl A G 1: 66,876,134 (GRCm39) Y396H probably benign Het
Apol7c A T 15: 77,410,318 (GRCm39) S209R possibly damaging Het
Atp1a1 A T 3: 101,484,308 (GRCm39) C990* probably null Het
Cachd1 C T 4: 100,825,295 (GRCm39) S583L probably damaging Het
Cbfa2t3 T C 8: 123,374,497 (GRCm39) T48A probably benign Het
Ccdc138 G T 10: 58,409,402 (GRCm39) probably benign Het
Cenpe A G 3: 134,970,112 (GRCm39) E2231G probably damaging Het
Cog3 T C 14: 75,979,129 (GRCm39) I206V probably damaging Het
Cr2 A G 1: 194,836,633 (GRCm39) probably benign Het
Ctdspl2 T C 2: 121,809,490 (GRCm39) V147A probably damaging Het
Cyp4f13 A G 17: 33,148,845 (GRCm39) V300A probably damaging Het
Dkk3 A T 7: 111,749,954 (GRCm39) M72K probably damaging Het
Dock3 A T 9: 106,900,944 (GRCm39) F340L probably benign Het
Fut1 A G 7: 45,268,127 (GRCm39) H27R possibly damaging Het
Igkv4-80 A G 6: 68,993,840 (GRCm39) V17A probably benign Het
Igkv9-123 G A 6: 67,931,380 (GRCm39) P62L possibly damaging Het
Kmt2e T C 5: 23,702,882 (GRCm39) S1021P probably damaging Het
Krt13 A C 11: 100,009,910 (GRCm39) L320R probably damaging Het
Ldhal6b T C 17: 5,467,819 (GRCm39) T372A probably benign Het
Manba T C 3: 135,250,510 (GRCm39) V379A probably benign Het
Map1b C T 13: 99,571,639 (GRCm39) V361I probably benign Het
Map4k1 A G 7: 28,693,531 (GRCm39) S399G probably benign Het
Mff G A 1: 82,724,815 (GRCm39) R229H probably damaging Het
Naga T C 15: 82,214,401 (GRCm39) N370S possibly damaging Het
Ncor2 A T 5: 125,102,621 (GRCm39) M2045K probably benign Het
Nipal1 T C 5: 72,805,250 (GRCm39) L7P probably damaging Het
Or10p22 T A 10: 128,825,958 (GRCm39) M59K probably damaging Het
Pcmt1 A T 10: 7,516,491 (GRCm39) M187K probably benign Het
Perp A T 10: 18,731,520 (GRCm39) T160S probably damaging Het
Rapgef6 G A 11: 54,516,690 (GRCm39) D169N probably damaging Het
Sel1l G A 12: 91,776,710 (GRCm39) Q711* probably null Het
Septin5 T C 16: 18,448,581 (GRCm39) Y7C probably damaging Het
Stard6 T A 18: 70,629,175 (GRCm39) probably benign Het
Sytl2 T C 7: 90,025,200 (GRCm39) V396A probably benign Het
Tcaf3 T G 6: 42,570,832 (GRCm39) M307L probably benign Het
Tdrd6 T C 17: 43,938,778 (GRCm39) N757D probably benign Het
Tgm1 T A 14: 55,947,446 (GRCm39) D305V probably damaging Het
Themis2 T A 4: 132,516,862 (GRCm39) M213L probably damaging Het
Tmem184c A G 8: 78,324,449 (GRCm39) V347A probably damaging Het
Tmem214 A G 5: 31,028,888 (GRCm39) E159G probably benign Het
Trim58 C T 11: 58,531,292 (GRCm39) probably benign Het
Tshz1 A T 18: 84,031,215 (GRCm39) S1064R probably damaging Het
Ubr2 C T 17: 47,268,266 (GRCm39) E983K possibly damaging Het
Vmn1r23 A T 6: 57,902,914 (GRCm39) I288N probably benign Het
Vmn2r97 T C 17: 19,149,947 (GRCm39) V445A probably benign Het
Whrn G A 4: 63,334,342 (GRCm39) T813M probably damaging Het
Xirp2 C T 2: 67,346,020 (GRCm39) H2754Y probably benign Het
Other mutations in Spdya
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01065:Spdya APN 17 71,863,320 (GRCm39) missense possibly damaging 0.51
IGL01667:Spdya APN 17 71,863,254 (GRCm39) start codon destroyed probably null 1.00
IGL02103:Spdya APN 17 71,885,242 (GRCm39) missense probably benign 0.15
IGL03220:Spdya APN 17 71,885,286 (GRCm39) missense possibly damaging 0.87
R0143:Spdya UTSW 17 71,865,635 (GRCm39) missense probably damaging 0.96
R0570:Spdya UTSW 17 71,869,585 (GRCm39) critical splice donor site probably null
R1666:Spdya UTSW 17 71,885,235 (GRCm39) missense probably damaging 1.00
R4019:Spdya UTSW 17 71,863,309 (GRCm39) missense possibly damaging 0.72
R4224:Spdya UTSW 17 71,869,519 (GRCm39) missense probably benign 0.07
R4225:Spdya UTSW 17 71,869,519 (GRCm39) missense probably benign 0.07
R4663:Spdya UTSW 17 71,885,339 (GRCm39) missense probably benign 0.04
R5013:Spdya UTSW 17 71,869,499 (GRCm39) missense possibly damaging 0.91
R5038:Spdya UTSW 17 71,895,561 (GRCm39) intron probably benign
R5583:Spdya UTSW 17 71,876,126 (GRCm39) missense probably damaging 0.99
R8323:Spdya UTSW 17 71,895,587 (GRCm39) missense probably benign 0.39
R9664:Spdya UTSW 17 71,869,513 (GRCm39) missense probably damaging 1.00
Posted On 2015-12-18