Incidental Mutation 'R6527:Sycp1'
ID 521942
Institutional Source Beutler Lab
Gene Symbol Sycp1
Ensembl Gene ENSMUSG00000027855
Gene Name synaptonemal complex protein 1
Synonyms SCP1
MMRRC Submission 044653-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.468) question?
Stock # R6527 (G1)
Quality Score 225.009
Status Not validated
Chromosome 3
Chromosomal Location 102818499-102936100 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 102898887 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 496 (V496A)
Ref Sequence ENSEMBL: ENSMUSP00000143651 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029448] [ENSMUST00000196988]
AlphaFold Q62209
Predicted Effect probably benign
Transcript: ENSMUST00000029448
AA Change: V496A

PolyPhen 2 Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: V496A

DomainStartEndE-ValueType
Pfam:SCP-1 28 809 N/A PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000196988
AA Change: V496A

PolyPhen 2 Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: V496A

DomainStartEndE-ValueType
Pfam:SCP-1 28 809 N/A PFAM
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 97.9%
  • 20x: 93.7%
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik A G 3: 138,067,527 (GRCm38) T826A probably damaging Het
Abca16 T A 7: 120,477,772 (GRCm38) I686N possibly damaging Het
Abcb6 T C 1: 75,177,488 (GRCm38) probably null Het
Adgrl3 A C 5: 81,787,517 (GRCm38) E1299A probably damaging Het
Als2cr12 T C 1: 58,692,413 (GRCm38) M1V probably null Het
Amd2 A C 10: 35,710,806 (GRCm38) Y252D probably damaging Het
Cfap74 A G 4: 155,422,265 (GRCm38) probably null Het
Dhx29 G T 13: 112,932,542 (GRCm38) K135N probably damaging Het
Dlg5 T A 14: 24,190,448 (GRCm38) D245V possibly damaging Het
Dscaml1 C T 9: 45,712,184 (GRCm38) Q83* probably null Het
Dsp T A 13: 38,195,873 (GRCm38) L1599Q probably damaging Het
Duox2 A G 2: 122,294,614 (GRCm38) V369A probably benign Het
Gbe1 T A 16: 70,433,672 (GRCm38) probably null Het
Gm7298 A G 6: 121,769,710 (GRCm38) K600R probably benign Het
Heatr4 C T 12: 83,979,763 (GRCm38) G240E probably damaging Het
Jakmip2 A G 18: 43,556,524 (GRCm38) V651A possibly damaging Het
Jam3 C T 9: 27,155,344 (GRCm38) R8Q unknown Het
Letm2 A G 8: 25,592,506 (GRCm38) probably benign Het
Lmod3 T C 6: 97,247,378 (GRCm38) D494G probably benign Het
Mast2 T C 4: 116,314,939 (GRCm38) D604G probably damaging Het
Mif4gd C T 11: 115,609,275 (GRCm38) probably null Het
Msr1 T C 8: 39,624,233 (GRCm38) E112G possibly damaging Het
Mtus2 A G 5: 148,277,598 (GRCm38) probably null Het
Muc4 A G 16: 32,753,433 (GRCm38) H1103R probably benign Het
Nudt14 T A 12: 112,934,887 (GRCm38) I198F possibly damaging Het
Olfr1341 T A 4: 118,709,848 (GRCm38) F147Y possibly damaging Het
Olfr353 T C 2: 36,890,582 (GRCm38) T89A probably benign Het
Olfr736 T A 14: 50,393,428 (GRCm38) L224* probably null Het
Osbpl8 T C 10: 111,293,205 (GRCm38) I884T probably benign Het
Podxl2 T C 6: 88,842,930 (GRCm38) N550S probably damaging Het
Ppp1r9a A G 6: 5,045,949 (GRCm38) Y151C probably damaging Het
Prss42 T C 9: 110,800,856 (GRCm38) V226A possibly damaging Het
Psmd12 A G 11: 107,488,968 (GRCm38) I116V probably damaging Het
Psme4 A C 11: 30,832,175 (GRCm38) I872L probably benign Het
Rab11fip1 A T 8: 27,174,392 (GRCm38) V65E probably damaging Het
Ros1 T C 10: 52,143,377 (GRCm38) N700S possibly damaging Het
Slc15a4 G A 5: 127,596,709 (GRCm38) T547M probably damaging Het
Slfn3 T A 11: 83,213,106 (GRCm38) C268S probably benign Het
Smc5 T C 19: 23,228,190 (GRCm38) Q794R probably benign Het
Sqor A G 2: 122,809,286 (GRCm38) Y434C probably damaging Het
Steap4 T A 5: 7,978,502 (GRCm38) L360H probably damaging Het
Tmem161b T G 13: 84,272,264 (GRCm38) M128R probably benign Het
Tmem59l T C 8: 70,486,125 (GRCm38) E102G probably damaging Het
Tnks A T 8: 34,873,093 (GRCm38) V457D probably benign Het
Tomt A G 7: 101,900,392 (GRCm38) Y230H probably damaging Het
Trim37 A G 11: 87,190,084 (GRCm38) N561D probably damaging Het
V1ra8 T A 6: 90,203,313 (GRCm38) I166K probably damaging Het
Vmn1r56 A G 7: 5,196,576 (GRCm38) V14A probably benign Het
Vsig8 T C 1: 172,560,358 (GRCm38) V5A possibly damaging Het
Vwa8 A T 14: 78,947,213 (GRCm38) S384C possibly damaging Het
Wwc1 C T 11: 35,853,437 (GRCm38) E853K probably benign Het
Zfp984 T C 4: 147,755,924 (GRCm38) N157D probably benign Het
Zzef1 G A 11: 72,874,990 (GRCm38) D1448N probably benign Het
Other mutations in Sycp1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00513:Sycp1 APN 3 102,840,962 (GRCm38) missense probably benign
IGL00833:Sycp1 APN 3 102,876,301 (GRCm38) critical splice donor site probably null
IGL01066:Sycp1 APN 3 102,920,634 (GRCm38) missense probably damaging 1.00
IGL01484:Sycp1 APN 3 102,915,867 (GRCm38) missense probably benign 0.01
IGL02139:Sycp1 APN 3 102,865,114 (GRCm38) missense probably benign 0.00
IGL02270:Sycp1 APN 3 102,895,943 (GRCm38) missense probably benign 0.12
IGL02347:Sycp1 APN 3 102,893,547 (GRCm38) missense probably benign 0.00
IGL02630:Sycp1 APN 3 102,878,764 (GRCm38) splice site probably benign
IGL02668:Sycp1 APN 3 102,820,531 (GRCm38) splice site probably benign
IGL02928:Sycp1 APN 3 102,818,818 (GRCm38) utr 3 prime probably benign
PIT4458001:Sycp1 UTSW 3 102,934,833 (GRCm38) missense probably benign 0.01
R0027:Sycp1 UTSW 3 102,895,910 (GRCm38) missense probably benign
R0282:Sycp1 UTSW 3 102,915,795 (GRCm38) splice site probably benign
R0462:Sycp1 UTSW 3 102,819,106 (GRCm38) missense possibly damaging 0.75
R0609:Sycp1 UTSW 3 102,898,849 (GRCm38) splice site probably null
R0837:Sycp1 UTSW 3 102,915,245 (GRCm38) missense probably benign 0.17
R1301:Sycp1 UTSW 3 102,920,622 (GRCm38) missense probably benign 0.02
R2408:Sycp1 UTSW 3 102,925,259 (GRCm38) missense probably damaging 1.00
R2449:Sycp1 UTSW 3 102,925,206 (GRCm38) missense probably benign 0.15
R2516:Sycp1 UTSW 3 102,845,066 (GRCm38) missense probably benign 0.09
R2880:Sycp1 UTSW 3 102,818,898 (GRCm38) missense probably damaging 0.99
R3410:Sycp1 UTSW 3 102,841,041 (GRCm38) missense possibly damaging 0.94
R3427:Sycp1 UTSW 3 102,876,350 (GRCm38) missense probably benign 0.00
R4538:Sycp1 UTSW 3 102,840,962 (GRCm38) missense probably benign
R4679:Sycp1 UTSW 3 102,922,462 (GRCm38) critical splice acceptor site probably null
R4707:Sycp1 UTSW 3 102,853,489 (GRCm38) missense possibly damaging 0.92
R4785:Sycp1 UTSW 3 102,853,489 (GRCm38) missense possibly damaging 0.92
R5017:Sycp1 UTSW 3 102,895,987 (GRCm38) splice site probably null
R5036:Sycp1 UTSW 3 102,820,600 (GRCm38) missense probably damaging 1.00
R5044:Sycp1 UTSW 3 102,845,054 (GRCm38) missense probably benign 0.03
R5070:Sycp1 UTSW 3 102,920,565 (GRCm38) missense probably damaging 0.97
R5079:Sycp1 UTSW 3 102,878,800 (GRCm38) missense possibly damaging 0.67
R5289:Sycp1 UTSW 3 102,934,253 (GRCm38) missense possibly damaging 0.85
R5393:Sycp1 UTSW 3 102,841,047 (GRCm38) splice site probably null
R5477:Sycp1 UTSW 3 102,818,890 (GRCm38) missense probably damaging 1.00
R5576:Sycp1 UTSW 3 102,818,902 (GRCm38) missense probably damaging 0.98
R5814:Sycp1 UTSW 3 102,895,897 (GRCm38) missense probably benign 0.03
R6291:Sycp1 UTSW 3 102,908,961 (GRCm38) missense probably damaging 1.00
R6460:Sycp1 UTSW 3 102,925,253 (GRCm38) missense probably damaging 1.00
R6870:Sycp1 UTSW 3 102,935,603 (GRCm38) missense probably damaging 1.00
R6873:Sycp1 UTSW 3 102,840,980 (GRCm38) missense probably benign
R7037:Sycp1 UTSW 3 102,898,934 (GRCm38) missense possibly damaging 0.62
R7210:Sycp1 UTSW 3 102,853,492 (GRCm38) missense probably damaging 1.00
R7405:Sycp1 UTSW 3 102,925,227 (GRCm38) missense possibly damaging 0.72
R7604:Sycp1 UTSW 3 102,913,433 (GRCm38) missense probably damaging 0.98
R7733:Sycp1 UTSW 3 102,895,962 (GRCm38) missense probably benign 0.00
R7858:Sycp1 UTSW 3 102,898,957 (GRCm38) missense probably benign 0.09
R7909:Sycp1 UTSW 3 102,820,626 (GRCm38) nonsense probably null
R8109:Sycp1 UTSW 3 102,851,602 (GRCm38) missense probably benign 0.21
R8141:Sycp1 UTSW 3 102,935,569 (GRCm38) missense possibly damaging 0.73
R8289:Sycp1 UTSW 3 102,841,037 (GRCm38) missense probably benign 0.01
R8359:Sycp1 UTSW 3 102,820,593 (GRCm38) missense probably damaging 0.98
R8844:Sycp1 UTSW 3 102,865,105 (GRCm38) missense probably damaging 1.00
R9020:Sycp1 UTSW 3 102,876,337 (GRCm38) missense probably benign 0.01
R9149:Sycp1 UTSW 3 102,851,628 (GRCm38) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGCTTTTGACTACAAAGCACG -3'
(R):5'- GCCAAATTTTCTCCAATGTATTGCTTG -3'

Sequencing Primer
(F):5'- GCTTCAGCTTCCAGAGTACTGAG -3'
(R):5'- GAGACTGTCTATGGAACTCCTGC -3'
Posted On 2018-06-06