Incidental Mutation 'R4663:Spdya'
ID 353050
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 041921-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.387) question?
Stock # R4663 (G1)
Quality Score 225
Status Not validated
Chromosome 17
Chromosomal Location 71859056-71896528 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 71885339 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 264 (S264R)
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: S264R

PolyPhen 2 Score 0.042 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000063214
Gene: ENSMUSG00000052525
AA Change: S264R

DomainStartEndE-ValueType
Pfam:Spy1 68 198 8.2e-63 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000124001
AA Change: S264R

PolyPhen 2 Score 0.042 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000118426
Gene: ENSMUSG00000052525
AA Change: S264R

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: S264R

PolyPhen 2 Score 0.042 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000118994
Gene: ENSMUSG00000052525
AA Change: S264R

DomainStartEndE-ValueType
Pfam:Spy1 68 198 2.2e-62 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000167641
AA Change: S264R

PolyPhen 2 Score 0.042 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000125912
Gene: ENSMUSG00000052525
AA Change: S264R

DomainStartEndE-ValueType
Pfam:Spy1 68 198 5.1e-69 PFAM
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.9%
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aqr A T 2: 113,992,147 (GRCm39) Y76* probably null Het
Armc5 C A 7: 127,837,717 (GRCm39) A140E probably benign Het
Auts2 T C 5: 131,468,476 (GRCm39) H947R probably damaging Het
Bag2 T C 1: 33,786,074 (GRCm39) T83A probably damaging Het
Bag4 C T 8: 26,259,516 (GRCm39) A228T probably benign Het
Bean1 A G 8: 104,937,799 (GRCm39) Y126C probably damaging Het
Cars1 T C 7: 143,129,697 (GRCm39) E330G probably damaging Het
Ccdc40 A G 11: 119,122,332 (GRCm39) I45V probably benign Het
Cd320 G A 17: 34,067,152 (GRCm39) G214R probably null Het
Ckm G A 7: 19,153,419 (GRCm39) V237M probably damaging Het
Cplane1 T C 15: 8,247,939 (GRCm39) V1496A probably benign Het
Cspg4 T C 9: 56,793,960 (GRCm39) V565A possibly damaging Het
Dnaaf10 T C 11: 17,182,853 (GRCm39) V338A probably benign Het
Eddm13 T G 7: 6,261,624 (GRCm39) I35S possibly damaging Het
Ephb6 A G 6: 41,594,799 (GRCm39) Y638C probably damaging Het
Fat2 G C 11: 55,187,039 (GRCm39) S1269* probably null Het
Fbxo3 T C 2: 103,883,820 (GRCm39) V348A probably damaging Het
Gas6 G A 8: 13,520,254 (GRCm39) P478L probably damaging Het
Herc1 T C 9: 66,340,660 (GRCm39) S1670P probably damaging Het
Hnrnpk C A 13: 58,542,331 (GRCm39) R281L probably damaging Het
Ifih1 C A 2: 62,439,563 (GRCm39) C488F probably benign Het
Ift172 T C 5: 31,441,559 (GRCm39) K192E probably benign Het
Ighv5-9 T A 12: 113,625,440 (GRCm39) Q101L probably benign Het
Igkv3-2 G T 6: 70,675,863 (GRCm39) M57I probably benign Het
Insyn2a A T 7: 134,500,877 (GRCm39) Y409* probably null Het
Itpr2 A G 6: 146,274,671 (GRCm39) F837S probably damaging Het
L3mbtl3 T C 10: 26,213,715 (GRCm39) Y237C unknown Het
Lats1 G A 10: 7,588,347 (GRCm39) C988Y probably damaging Het
Lgals3 T A 14: 47,619,079 (GRCm39) probably null Het
Lrrc3b G T 14: 15,358,220 (GRCm38) H129N probably benign Het
Lrriq1 T C 10: 102,899,273 (GRCm39) H1656R possibly damaging Het
Lypd6 T G 2: 50,063,623 (GRCm39) Y43* probably null Het
Mettl25b A G 3: 87,835,055 (GRCm39) S82P probably damaging Het
Mical2 A G 7: 111,927,884 (GRCm39) D674G possibly damaging Het
Msi1 G A 5: 115,588,334 (GRCm39) R284Q probably damaging Het
Mybpc2 T C 7: 44,155,066 (GRCm39) E947G probably damaging Het
Nat14 T A 7: 4,927,446 (GRCm39) L206Q probably damaging Het
Nup88 A T 11: 70,856,672 (GRCm39) probably null Het
Or11g27 A T 14: 50,771,061 (GRCm39) Y64F probably damaging Het
Or4k15 A G 14: 50,364,939 (GRCm39) R302G probably benign Het
Or8g19 A T 9: 39,056,145 (GRCm39) I250F probably damaging Het
Pdcl T C 2: 37,245,778 (GRCm39) E75G probably damaging Het
Phf14 A G 6: 11,953,421 (GRCm39) I387V possibly damaging Het
Phf3 G A 1: 30,860,296 (GRCm39) R845W probably damaging Het
Pm20d1 T C 1: 131,726,340 (GRCm39) I59T probably damaging Het
Prkd1 C T 12: 50,466,631 (GRCm39) probably null Het
Psmb2 T C 4: 126,571,558 (GRCm39) L4P probably damaging Het
Pttg1 T A 11: 43,315,677 (GRCm39) K46* probably null Het
Ryr2 T C 13: 11,764,395 (GRCm39) H1401R possibly damaging Het
Septin4 T A 11: 87,458,429 (GRCm39) Y268N probably damaging Het
Sh3d19 G A 3: 86,030,570 (GRCm39) D696N probably benign Het
Slc16a2 T C X: 102,751,585 (GRCm39) T274A probably benign Het
Slc26a6 G A 9: 108,735,106 (GRCm39) A335T probably damaging Het
Slc49a3 T C 5: 108,590,011 (GRCm39) M464V probably benign Het
Slc6a5 C A 7: 49,588,146 (GRCm39) Y493* probably null Het
Slf1 A T 13: 77,274,723 (GRCm39) S37R probably damaging Het
Smoc1 G A 12: 81,214,376 (GRCm39) G264S probably damaging Het
Snapc4 T C 2: 26,264,193 (GRCm39) E280G possibly damaging Het
Snx25 G A 8: 46,488,616 (GRCm39) T913M probably damaging Het
Snx7 T C 3: 117,594,528 (GRCm39) T408A probably benign Het
Spg11 A T 2: 121,928,580 (GRCm39) probably null Het
Suz12 T A 11: 79,904,350 (GRCm39) L230Q probably damaging Het
Szt2 A G 4: 118,234,881 (GRCm39) probably benign Het
Tenm3 C A 8: 48,689,005 (GRCm39) R2194L probably damaging Het
Tmed8 T A 12: 87,221,005 (GRCm39) I194F probably damaging Het
Tmem79 T A 3: 88,240,751 (GRCm39) T66S probably damaging Het
Trappc1 T A 11: 69,216,337 (GRCm39) S118T probably benign Het
Ttn C T 2: 76,569,225 (GRCm39) V27223I probably benign Het
Ttn T C 2: 76,606,839 (GRCm39) T18024A probably damaging Het
Vmn2r15 C T 5: 109,441,940 (GRCm39) M164I probably benign Het
Vmn2r53 T A 7: 12,334,901 (GRCm39) Y253F probably benign Het
Zfand6 C T 7: 84,267,093 (GRCm39) R163H 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
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
R4225:Spdya UTSW 17 71,869,519 (GRCm39) missense probably benign 0.07
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'- TTACATCTGGCAACGAGAGCG -3'
(R):5'- GGCTAGCACAACATGGGTATAG -3'

Sequencing Primer
(F):5'- TGTGCATCACAGTGGAGC -3'
(R):5'- CTAGCACAACATGGGTATAGATAGG -3'
Posted On 2015-10-08