Incidental Mutation 'R9020:Sycp1'
ID 686644
Institutional Source Beutler Lab
Gene Symbol Sycp1
Ensembl Gene ENSMUSG00000027855
Gene Name synaptonemal complex protein 1
Synonyms SCP1
MMRRC Submission 068850-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.539) question?
Stock # R9020 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 102725815-102843416 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 102783653 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Arginine at position 607 (K607R)
Ref Sequence ENSEMBL: ENSMUSP00000029448 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029448] [ENSMUST00000196988]
AlphaFold Q62209
Predicted Effect probably benign
Transcript: ENSMUST00000029448
AA Change: K607R

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: K607R

DomainStartEndE-ValueType
Pfam:SCP-1 28 809 N/A PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000196988
AA Change: K607R

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: K607R

DomainStartEndE-ValueType
Pfam:SCP-1 28 809 N/A PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency 97% (58/60)
MGI Phenotype PHENOTYPE: Homozygous null mice display male and female infertility, azoospermia, small ovary, small testis and seminiferous tubules, absent ovarian follicles, and failure of synapse formation during meiosis. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acot11 A G 4: 106,605,615 (GRCm39) S586P probably damaging Het
Adora3 T A 3: 105,815,141 (GRCm39) I297N probably damaging Het
Adrb3 A T 8: 27,717,947 (GRCm39) F167L probably damaging Het
Apob A G 12: 8,063,999 (GRCm39) Y3955C probably damaging Het
Atp2a1 T C 7: 126,046,135 (GRCm39) D963G probably benign Het
Btbd10 T C 7: 112,951,057 (GRCm39) N11S possibly damaging Het
Casr A G 16: 36,315,611 (GRCm39) S820P probably damaging Het
Ccdc82 C T 9: 13,281,915 (GRCm39) R447C probably damaging Het
Cfap44 T A 16: 44,257,522 (GRCm39) V1019E probably damaging Het
Cfap65 T C 1: 74,959,552 (GRCm39) E866G probably damaging Het
Chd4 T A 6: 125,084,469 (GRCm39) D713E probably damaging Het
Ctdsp1 T C 1: 74,434,676 (GRCm39) F240S possibly damaging Het
Cyp26b1 C T 6: 84,552,056 (GRCm39) V361I probably benign Het
Dmbt1 T A 7: 130,712,787 (GRCm39) I1597N possibly damaging Het
Dnajc25 C A 4: 59,003,470 (GRCm39) Y80* probably null Het
Fbxo17 A T 7: 28,436,782 (GRCm39) N246Y possibly damaging Het
Filip1l A G 16: 57,391,058 (GRCm39) T549A probably benign Het
Gm9758 A C 5: 14,964,739 (GRCm39) N35K Het
Gtf2i T C 5: 134,275,415 (GRCm39) T707A probably benign Het
Ifnk T C 4: 35,152,573 (GRCm39) V167A probably damaging Het
Iqch T C 9: 63,432,526 (GRCm39) M290V probably benign Het
Irx1 A T 13: 72,111,548 (GRCm39) Y20* probably null Het
Jade2 T A 11: 51,708,454 (GRCm39) Q572L probably benign Het
Kcne4 T A 1: 78,795,425 (GRCm39) H24Q probably benign Het
Kcnq5 T C 1: 21,539,463 (GRCm39) probably benign Het
Kcnt2 T A 1: 140,512,049 (GRCm39) V1068E probably benign Het
Klk1b27 T A 7: 43,705,118 (GRCm39) V95D probably damaging Het
Lins1 A G 7: 66,357,961 (GRCm39) D32G probably damaging Het
Mavs A G 2: 131,088,594 (GRCm39) E466G possibly damaging Het
Mipep T A 14: 61,068,677 (GRCm39) L483* probably null Het
Muc16 G GAATGGCTTTCTT 9: 18,550,015 (GRCm39) probably benign Het
Myo1a C A 10: 127,549,992 (GRCm39) Q491K probably benign Het
Nle1 C G 11: 82,797,275 (GRCm39) E146Q probably benign Het
Nphp3 T C 9: 103,909,150 (GRCm39) Y787H probably benign Het
Pcdh15 A G 10: 74,481,443 (GRCm39) S263G probably benign Het
Pcdhb8 T G 18: 37,489,837 (GRCm39) I505S probably damaging Het
Phtf1 C G 3: 103,898,694 (GRCm39) S339* probably null Het
Pip5k1b T A 19: 24,327,585 (GRCm39) I424F probably benign Het
Plxna4 T A 6: 32,211,497 (GRCm39) T681S possibly damaging Het
Prdm1 A G 10: 44,316,036 (GRCm39) L700P probably damaging Het
Prtg C T 9: 72,799,277 (GRCm39) T769I probably damaging Het
Rasgrf2 A G 13: 92,165,146 (GRCm39) V340A possibly damaging Het
Ros1 T A 10: 52,031,023 (GRCm39) E548D probably benign Het
Rsph10b G A 5: 143,922,283 (GRCm39) R823Q probably benign Het
Scgb1b3 A G 7: 31,075,276 (GRCm39) E42G probably damaging Het
Scyl2 T C 10: 89,488,858 (GRCm39) N486D probably damaging Het
Sdr9c7 T A 10: 127,745,659 (GRCm39) I257N possibly damaging Het
Serpinb9b A T 13: 33,223,887 (GRCm39) I360F probably damaging Het
Slc15a5 T A 6: 138,032,704 (GRCm39) I217F probably benign Het
Steap2 T C 5: 5,723,480 (GRCm39) S467G probably benign Het
Tek C G 4: 94,708,339 (GRCm39) P350R probably benign Het
Tet3 T C 6: 83,381,418 (GRCm39) D250G probably damaging Het
Trip11 A G 12: 101,850,770 (GRCm39) V1098A possibly damaging Het
Tsc2 G T 17: 24,845,691 (GRCm39) T209K probably damaging Het
Ttc6 A G 12: 57,752,366 (GRCm39) Y1424C probably damaging Het
Uchl3 A T 14: 101,903,986 (GRCm39) K74N probably damaging Het
Usp10 T G 8: 120,667,904 (GRCm39) S68R probably benign Het
Wwp1 T C 4: 19,650,282 (GRCm39) I295V probably benign Het
Other mutations in Sycp1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00513:Sycp1 APN 3 102,748,278 (GRCm39) missense probably benign
IGL00833:Sycp1 APN 3 102,783,617 (GRCm39) critical splice donor site probably null
IGL01066:Sycp1 APN 3 102,827,950 (GRCm39) missense probably damaging 1.00
IGL01484:Sycp1 APN 3 102,823,183 (GRCm39) missense probably benign 0.01
IGL02139:Sycp1 APN 3 102,772,430 (GRCm39) missense probably benign 0.00
IGL02270:Sycp1 APN 3 102,803,259 (GRCm39) missense probably benign 0.12
IGL02347:Sycp1 APN 3 102,800,863 (GRCm39) missense probably benign 0.00
IGL02630:Sycp1 APN 3 102,786,080 (GRCm39) splice site probably benign
IGL02668:Sycp1 APN 3 102,727,847 (GRCm39) splice site probably benign
IGL02928:Sycp1 APN 3 102,726,134 (GRCm39) utr 3 prime probably benign
PIT4458001:Sycp1 UTSW 3 102,842,149 (GRCm39) missense probably benign 0.01
R0027:Sycp1 UTSW 3 102,803,226 (GRCm39) missense probably benign
R0282:Sycp1 UTSW 3 102,823,111 (GRCm39) splice site probably benign
R0462:Sycp1 UTSW 3 102,726,422 (GRCm39) missense possibly damaging 0.75
R0609:Sycp1 UTSW 3 102,806,165 (GRCm39) splice site probably null
R0837:Sycp1 UTSW 3 102,822,561 (GRCm39) missense probably benign 0.17
R1301:Sycp1 UTSW 3 102,827,938 (GRCm39) missense probably benign 0.02
R2408:Sycp1 UTSW 3 102,832,575 (GRCm39) missense probably damaging 1.00
R2449:Sycp1 UTSW 3 102,832,522 (GRCm39) missense probably benign 0.15
R2516:Sycp1 UTSW 3 102,752,382 (GRCm39) missense probably benign 0.09
R2880:Sycp1 UTSW 3 102,726,214 (GRCm39) missense probably damaging 0.99
R3410:Sycp1 UTSW 3 102,748,357 (GRCm39) missense possibly damaging 0.94
R3427:Sycp1 UTSW 3 102,783,666 (GRCm39) missense probably benign 0.00
R4538:Sycp1 UTSW 3 102,748,278 (GRCm39) missense probably benign
R4679:Sycp1 UTSW 3 102,829,778 (GRCm39) critical splice acceptor site probably null
R4707:Sycp1 UTSW 3 102,760,805 (GRCm39) missense possibly damaging 0.92
R4785:Sycp1 UTSW 3 102,760,805 (GRCm39) missense possibly damaging 0.92
R5017:Sycp1 UTSW 3 102,803,303 (GRCm39) splice site probably null
R5036:Sycp1 UTSW 3 102,727,916 (GRCm39) missense probably damaging 1.00
R5044:Sycp1 UTSW 3 102,752,370 (GRCm39) missense probably benign 0.03
R5070:Sycp1 UTSW 3 102,827,881 (GRCm39) missense probably damaging 0.97
R5079:Sycp1 UTSW 3 102,786,116 (GRCm39) missense possibly damaging 0.67
R5289:Sycp1 UTSW 3 102,841,569 (GRCm39) missense possibly damaging 0.85
R5393:Sycp1 UTSW 3 102,748,363 (GRCm39) splice site probably null
R5477:Sycp1 UTSW 3 102,726,206 (GRCm39) missense probably damaging 1.00
R5576:Sycp1 UTSW 3 102,726,218 (GRCm39) missense probably damaging 0.98
R5814:Sycp1 UTSW 3 102,803,213 (GRCm39) missense probably benign 0.03
R6291:Sycp1 UTSW 3 102,816,277 (GRCm39) missense probably damaging 1.00
R6460:Sycp1 UTSW 3 102,832,569 (GRCm39) missense probably damaging 1.00
R6527:Sycp1 UTSW 3 102,806,203 (GRCm39) missense probably benign 0.09
R6870:Sycp1 UTSW 3 102,842,919 (GRCm39) missense probably damaging 1.00
R6873:Sycp1 UTSW 3 102,748,296 (GRCm39) missense probably benign
R7037:Sycp1 UTSW 3 102,806,250 (GRCm39) missense possibly damaging 0.62
R7210:Sycp1 UTSW 3 102,760,808 (GRCm39) missense probably damaging 1.00
R7405:Sycp1 UTSW 3 102,832,543 (GRCm39) missense possibly damaging 0.72
R7604:Sycp1 UTSW 3 102,820,749 (GRCm39) missense probably damaging 0.98
R7733:Sycp1 UTSW 3 102,803,278 (GRCm39) missense probably benign 0.00
R7858:Sycp1 UTSW 3 102,806,273 (GRCm39) missense probably benign 0.09
R7909:Sycp1 UTSW 3 102,727,942 (GRCm39) nonsense probably null
R8109:Sycp1 UTSW 3 102,758,918 (GRCm39) missense probably benign 0.21
R8141:Sycp1 UTSW 3 102,842,885 (GRCm39) missense possibly damaging 0.73
R8289:Sycp1 UTSW 3 102,748,353 (GRCm39) missense probably benign 0.01
R8359:Sycp1 UTSW 3 102,727,909 (GRCm39) missense probably damaging 0.98
R8844:Sycp1 UTSW 3 102,772,421 (GRCm39) missense probably damaging 1.00
R9149:Sycp1 UTSW 3 102,758,944 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TGGTGAATCCAGAGTTTCTTCAAAGAA -3'
(R):5'- AGGTAGTTAACAGTCACATAAAGGT -3'

Sequencing Primer
(F):5'- ACTGGCTGCTCTTTCAGAGGAC -3'
(R):5'- GGACAATGAAACAAACTGGATAT -3'
Posted On 2021-11-19