Incidental Mutation 'R7405:Sycp1'
ID 574490
Institutional Source Beutler Lab
Gene Symbol Sycp1
Ensembl Gene ENSMUSG00000027855
Gene Name synaptonemal complex protein 1
Synonyms SCP1
MMRRC Submission 045376-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.539) question?
Stock # R7405 (G1)
Quality Score 225.009
Status Not validated
Chromosome 3
Chromosomal Location 102725815-102843416 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 102832543 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 208 (Y208H)
Ref Sequence ENSEMBL: ENSMUSP00000029448 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029448] [ENSMUST00000196988] [ENSMUST00000199930]
AlphaFold Q62209
Predicted Effect possibly damaging
Transcript: ENSMUST00000029448
AA Change: Y208H

PolyPhen 2 Score 0.722 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: Y208H

DomainStartEndE-ValueType
Pfam:SCP-1 28 809 N/A PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000196988
AA Change: Y208H

PolyPhen 2 Score 0.722 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: Y208H

DomainStartEndE-ValueType
Pfam:SCP-1 28 809 N/A PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000199930
AA Change: Y153H

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000143493
Gene: ENSMUSG00000027855
AA Change: Y153H

DomainStartEndE-ValueType
Pfam:SCP-1 28 95 2e-33 PFAM
Pfam:SCP-1 93 182 9.8e-53 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.4%
Validation Efficiency
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: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700010I14Rik G T 17: 9,220,649 (GRCm39) V383L probably damaging Het
4930507D05Rik C A 10: 62,285,563 (GRCm39) H96N unknown Het
5730480H06Rik T C 5: 48,545,458 (GRCm39) I235T possibly damaging Het
Abcb11 A G 2: 69,117,963 (GRCm39) Y472H probably damaging Het
Adam39 A T 8: 41,277,659 (GRCm39) I17L probably benign Het
Aire T C 10: 77,870,447 (GRCm39) H458R probably benign Het
Ap3d1 T C 10: 80,577,734 (GRCm39) D31G probably benign Het
Atad2b T A 12: 4,993,232 (GRCm39) H250Q probably benign Het
Bnip5 G A 17: 29,124,298 (GRCm39) R335W probably damaging Het
Borcs5 C A 6: 134,662,945 (GRCm39) T74N probably benign Het
Btbd16 C T 7: 130,407,586 (GRCm39) T292I probably benign Het
Catsperd G A 17: 56,939,335 (GRCm39) V55M possibly damaging Het
Cfap107 T C 4: 144,146,323 (GRCm39) N110S probably damaging Het
Ctr9 T C 7: 110,642,921 (GRCm39) F462S possibly damaging Het
Cyp4f39 A G 17: 32,700,789 (GRCm39) S153G probably benign Het
Ddo T C 10: 40,523,993 (GRCm39) C328R possibly damaging Het
Ddr1 A G 17: 36,000,992 (GRCm39) V251A probably damaging Het
Dis3l A G 9: 64,221,986 (GRCm39) F475L probably damaging Het
Dkk4 G A 8: 23,115,859 (GRCm39) V99M probably benign Het
Dync1h1 C T 12: 110,600,654 (GRCm39) A1938V probably damaging Het
Ecel1 A T 1: 87,081,238 (GRCm39) probably null Het
Fbxo7 T A 10: 85,880,445 (GRCm39) Y377N probably damaging Het
Fbxw24 T C 9: 109,436,136 (GRCm39) I299V possibly damaging Het
Fkbp10 C T 11: 100,306,707 (GRCm39) A33V probably damaging Het
Gabra1 T C 11: 42,045,850 (GRCm39) T87A probably damaging Het
Gm21886 ACTCACTGAGGCCTGCAGACAGTAGGTGCTCACTGAGGCCTGCAGACAGTAGGTGCTCACTGAGGCCTGCAGACAGTAGGTGCTCACTGAGACCTGCAGACAGTAGGTGCTCACTGAGACCTGCAGACAGTAGGTGCTCACTGAGG ACTCACTGAGGCCTGCAGACAGTAGGTGCTCACTGAGGCCTGCAGACAGTAGGTGCTCACTGAGACCTGCAGACAGTAGGTGCTCACTGAGACCTGCAGACAGTAGGTGCTCACTGAGG 18: 80,133,040 (GRCm39) probably benign Het
Golga3 A T 5: 110,356,312 (GRCm39) I1000F probably damaging Het
Grid2ip T C 5: 143,366,199 (GRCm39) I563T probably benign Het
Gsx1 T C 5: 147,125,943 (GRCm39) S82P possibly damaging Het
Heg1 A G 16: 33,583,819 (GRCm39) K34E possibly damaging Het
Kank1 T A 19: 25,387,683 (GRCm39) L452* probably null Het
Lce1k A T 3: 92,714,181 (GRCm39) M1K probably null Het
Lcmt2 A G 2: 120,969,868 (GRCm39) I185T probably benign Het
Lrp1 T C 10: 127,417,620 (GRCm39) D1046G possibly damaging Het
Lrrc37 A T 11: 103,505,987 (GRCm39) Y1994N probably benign Het
Mast3 A T 8: 71,238,815 (GRCm39) D496E probably damaging Het
Mst1r C T 9: 107,792,321 (GRCm39) S925F possibly damaging Het
Mterf2 C T 10: 84,956,360 (GRCm39) G88D probably damaging Het
Mthfd1 T C 12: 76,358,648 (GRCm39) V783A probably damaging Het
Mybpc2 A T 7: 44,156,618 (GRCm39) W778R probably damaging Het
Nbea A G 3: 55,712,687 (GRCm39) L2130P possibly damaging Het
Ndst4 A G 3: 125,476,865 (GRCm39) N30S probably benign Het
Nphs1 T C 7: 30,162,253 (GRCm39) V299A possibly damaging Het
Nup107 T C 10: 117,606,320 (GRCm39) D474G probably benign Het
Or10ag56 A C 2: 87,139,339 (GRCm39) I89L probably benign Het
Or10w1 T C 19: 13,632,246 (GRCm39) V151A probably benign Het
Or2w25 T A 11: 59,504,899 (GRCm39) F370I possibly damaging Het
Or7a42 T C 10: 78,791,531 (GRCm39) V164A probably benign Het
Pgap2 T C 7: 101,880,595 (GRCm39) V41A probably benign Het
Plekhh1 C T 12: 79,101,821 (GRCm39) T297I probably benign Het
Plxna4 A T 6: 32,173,254 (GRCm39) Y1226N probably benign Het
Polr3b A G 10: 84,520,043 (GRCm39) D653G probably benign Het
Ppp2r2c T C 5: 37,104,486 (GRCm39) F289L possibly damaging Het
Prickle2 A G 6: 92,435,524 (GRCm39) S82P probably damaging Het
Ptger2 T A 14: 45,226,531 (GRCm39) V37D probably damaging Het
Rasa2 G A 9: 96,448,080 (GRCm39) P526S probably benign Het
Rbm47 A T 5: 66,183,838 (GRCm39) I255N probably damaging Het
Sez6 A T 11: 77,853,717 (GRCm39) T296S probably benign Het
Slc2a9 T A 5: 38,549,167 (GRCm39) I316F probably damaging Het
Slc41a1 T A 1: 131,766,884 (GRCm39) V134D probably damaging Het
Slc5a7 A T 17: 54,604,161 (GRCm39) S2T probably benign Het
Slc9a4 C T 1: 40,640,086 (GRCm39) R293C probably damaging Het
Son CATGGACTCCCAGATGTTAGCAACTAGCTCTATGGACTCCCAGATGTTAGCAACTAGCTCTATGGACTCCCAGATGTTAGCAACCAGCAGTATGGACTCCCAGATGTTAGCAACCAGCAGTATGGACTCCCAGATGTTAGCAACCAGCTCCATGGACTCCCAGATGTTAGCAAC CATGGACTCCCAGATGTTAGCAACTAGCTCTATGGACTCCCAGATGTTAGCAACCAGCAGTATGGACTCCCAGATGTTAGCAACCAGCAGTATGGACTCCCAGATGTTAGCAACCAGCTCCATGGACTCCCAGATGTTAGCAAC 16: 91,453,579 (GRCm39) probably benign Het
Suco A G 1: 161,655,783 (GRCm39) F1039L possibly damaging Het
Tpr T C 1: 150,317,878 (GRCm39) S2129P probably benign Het
Trim34b T A 7: 103,985,690 (GRCm39) S442T probably damaging Het
Ttn A T 2: 76,573,690 (GRCm39) Y25734* probably null Het
Uchl5 C T 1: 143,675,752 (GRCm39) Q276* probably null Het
Wrn C G 8: 33,738,994 (GRCm39) W1278S probably benign Het
Yeats2 T A 16: 20,041,663 (GRCm39) D1184E probably damaging Het
Zfat G A 15: 68,056,334 (GRCm39) R241W probably damaging Het
Zfp646 T A 7: 127,477,968 (GRCm39) Y48* probably null Het
Zfp998 T C 13: 66,579,118 (GRCm39) Q455R unknown 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
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
R9020:Sycp1 UTSW 3 102,783,653 (GRCm39) missense probably benign 0.01
R9149:Sycp1 UTSW 3 102,758,944 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TTTACTGGTGATTCAACCATGCATC -3'
(R):5'- AAACTTGTAAGGATGTTGTGCC -3'

Sequencing Primer
(F):5'- AGCTATCACTCTTTCTGCTTAG -3'
(R):5'- GCAATGCCAGTTACAGTTCAG -3'
Posted On 2019-09-13