Incidental Mutation 'R4225:Spdya'
ID 320016
Institutional Source Beutler Lab
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
MMRRC Submission 041045-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.387) question?
Stock # R4225 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 71859056-71896528 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 71869519 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Isoleucine at position 105 (V105I)
Ref Sequence ENSEMBL: ENSMUSP00000125912 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000064420] [ENSMUST00000124001] [ENSMUST00000144142] [ENSMUST00000167641]
AlphaFold Q5IBH7
Predicted Effect probably benign
Transcript: ENSMUST00000064420
AA Change: V105I

PolyPhen 2 Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000063214
Gene: ENSMUSG00000052525
AA Change: V105I

DomainStartEndE-ValueType
Pfam:Spy1 68 198 8.2e-63 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000124001
AA Change: V105I

PolyPhen 2 Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000118426
Gene: ENSMUSG00000052525
AA Change: V105I

DomainStartEndE-ValueType
Pfam:Spy1 68 198 1.5e-69 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130952
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137830
Predicted Effect probably benign
Transcript: ENSMUST00000144142
AA Change: V105I

PolyPhen 2 Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000118994
Gene: ENSMUSG00000052525
AA Change: V105I

DomainStartEndE-ValueType
Pfam:Spy1 68 198 2.2e-62 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000167641
AA Change: V105I

PolyPhen 2 Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000125912
Gene: ENSMUSG00000052525
AA Change: V105I

DomainStartEndE-ValueType
Pfam:Spy1 68 198 5.1e-69 PFAM
Meta Mutation Damage Score 0.0710 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.6%
  • 20x: 96.1%
Validation Efficiency 100% (38/38)
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: 34 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca1 T C 4: 53,085,106 (GRCm39) I569V possibly damaging Het
Aif1l A T 2: 31,852,251 (GRCm39) S40C probably damaging Het
Arhgef26 A G 3: 62,288,343 (GRCm39) D471G probably benign Het
Atp2a2 A G 5: 122,607,789 (GRCm39) V240A probably benign Het
Bsn A G 9: 107,983,932 (GRCm39) M3374T unknown Het
Ccdc66 A G 14: 27,212,736 (GRCm39) L529P probably damaging Het
Ctif A G 18: 75,568,308 (GRCm39) I610T probably benign Het
Ecpas A T 4: 58,847,027 (GRCm39) Y512N probably damaging Het
Eif3c C G 7: 126,165,471 (GRCm39) probably benign Het
Esyt1 T C 10: 128,356,517 (GRCm39) Y376C probably damaging Het
Gba2 A T 4: 43,569,464 (GRCm39) probably benign Het
Grin1 T C 2: 25,187,332 (GRCm39) probably benign Het
Herc2 A G 7: 55,814,735 (GRCm39) E2696G probably damaging Het
Itgal A T 7: 126,904,484 (GRCm39) K319M probably damaging Het
Lama3 T C 18: 12,583,460 (GRCm39) C683R probably damaging Het
Lrig1 T A 6: 94,599,639 (GRCm39) I348F probably damaging Het
Mc3r G A 2: 172,090,954 (GRCm39) V59M probably damaging Het
Msh3 T C 13: 92,422,431 (GRCm39) K575R probably benign Het
Musk A T 4: 58,373,240 (GRCm39) M714L probably damaging Het
Odad2 A G 18: 7,181,732 (GRCm39) probably null Het
Pcdhgb7 T A 18: 37,886,856 (GRCm39) D675E probably benign Het
Pkd1 T C 17: 24,812,497 (GRCm39) I3810T possibly damaging Het
Pou2f1 T C 1: 165,738,889 (GRCm39) I177V possibly damaging Het
Rb1 T C 14: 73,506,631 (GRCm39) M373V possibly damaging Het
Ric1 A G 19: 29,580,131 (GRCm39) N1311D possibly damaging Het
Scn3a A G 2: 65,366,771 (GRCm39) Y84H probably damaging Het
Slc25a45 A T 19: 5,930,146 (GRCm39) I39F probably damaging Het
Slc8a1 A G 17: 81,956,781 (GRCm39) F86L probably damaging Het
Sspo G T 6: 48,428,091 (GRCm39) V313L possibly damaging Het
Stard9 A G 2: 120,495,472 (GRCm39) T116A possibly damaging Het
Stpg2 G A 3: 138,921,053 (GRCm39) R86Q probably damaging Het
Tdrd6 C T 17: 43,936,864 (GRCm39) D1395N probably damaging Het
Vmn2r101 T A 17: 19,831,951 (GRCm39) I649N probably damaging Het
Zcchc18 A T X: 135,895,415 (GRCm39) N10I probably damaging 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
IGL02934:Spdya APN 17 71,863,395 (GRCm39) missense probably benign 0.01
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
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
Predicted Primers PCR Primer
(F):5'- TTCAAGTGGATTAACTCTGGGG -3'
(R):5'- TGGCATGTAATGTAAGGCCAATG -3'

Sequencing Primer
(F):5'- GTACTCAGGTGACTGTATACAG -3'
(R):5'- TAATTTTCCCACACAAGATGGC -3'
Posted On 2015-06-12