Incidental Mutation 'IGL02103:Sycp3'
ID 279839
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Sycp3
Ensembl Gene ENSMUSG00000020059
Gene Name synaptonemal complex protein 3
Synonyms Scp3, Cor1
Accession Numbers
Essential gene? Probably non essential (E-score: 0.127) question?
Stock # IGL02103
Quality Score
Status
Chromosome 10
Chromosomal Location 88295449-88309098 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 88302334 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Arginine at position 108 (K108R)
Ref Sequence ENSEMBL: ENSMUSP00000137800 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020252] [ENSMUST00000117440] [ENSMUST00000123244] [ENSMUST00000125612] [ENSMUST00000148899]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000020252
AA Change: K108R

PolyPhen 2 Score 0.648 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000020252
Gene: ENSMUSG00000020059
AA Change: K108R

DomainStartEndE-ValueType
low complexity region 42 53 N/A INTRINSIC
Pfam:Cor1 101 229 6.1e-57 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000117440
SMART Domains Protein: ENSMUSP00000112708
Gene: ENSMUSG00000060002

DomainStartEndE-ValueType
low complexity region 2 12 N/A INTRINSIC
Pfam:CDP-OH_P_transf 61 136 8.8e-18 PFAM
transmembrane domain 159 181 N/A INTRINSIC
transmembrane domain 191 213 N/A INTRINSIC
transmembrane domain 226 248 N/A INTRINSIC
transmembrane domain 263 282 N/A INTRINSIC
transmembrane domain 295 317 N/A INTRINSIC
transmembrane domain 349 371 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000123244
SMART Domains Protein: ENSMUSP00000137704
Gene: ENSMUSG00000020059

DomainStartEndE-ValueType
low complexity region 42 53 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000125612
AA Change: K108R

PolyPhen 2 Score 0.648 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000137800
Gene: ENSMUSG00000020059
AA Change: K108R

DomainStartEndE-ValueType
low complexity region 42 53 N/A INTRINSIC
Pfam:Cor1 100 229 7.6e-60 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000134318
SMART Domains Protein: ENSMUSP00000122428
Gene: ENSMUSG00000060002

DomainStartEndE-ValueType
transmembrane domain 20 42 N/A INTRINSIC
transmembrane domain 55 77 N/A INTRINSIC
transmembrane domain 109 131 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000148899
SMART Domains Protein: ENSMUSP00000120167
Gene: ENSMUSG00000060002

DomainStartEndE-ValueType
transmembrane domain 25 47 N/A INTRINSIC
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an essential structural component of the synaptonemal complex. This complex is involved in synapsis, recombination and segregation of meiotic chromosomes. Mutations in this gene are associated with azoospermia in males and susceptibility to pregnancy loss in females. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, May 2010]
PHENOTYPE: Homozygous mutants are male infertile and female sub-fertile. Reduced litter size in females is due to achiasmatic oocytes, resulting in aneuploidy and embryonic death. Meiosis in males blocks at early prophase with lack of synaptonemal complexes. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcd4 G A 12: 84,659,138 (GRCm39) T206M probably benign Het
Adcy3 T A 12: 4,184,390 (GRCm39) V22D possibly damaging Het
Alb G A 5: 90,611,990 (GRCm39) E140K probably benign Het
Aph1a G A 3: 95,803,125 (GRCm39) V193I probably damaging Het
Asb2 G A 12: 103,299,755 (GRCm39) R178* probably null Het
Celf3 A T 3: 94,394,108 (GRCm39) Q137L probably damaging Het
Cmya5 T C 13: 93,228,635 (GRCm39) D2151G probably benign Het
Cuedc1 T A 11: 88,079,625 (GRCm39) S353T probably damaging Het
Dlg5 A C 14: 24,194,414 (GRCm39) L1709R probably damaging Het
Dst T C 1: 34,229,199 (GRCm39) I1939T possibly damaging Het
Emx2 A T 19: 59,450,130 (GRCm39) N149I probably benign Het
Fancm A G 12: 65,142,558 (GRCm39) D472G probably benign Het
Fasn T C 11: 120,702,762 (GRCm39) Y1700C probably damaging Het
Fat2 T A 11: 55,180,122 (GRCm39) R1406S probably damaging Het
Fat4 C A 3: 38,943,348 (GRCm39) T747K probably damaging Het
Fer A G 17: 64,445,923 (GRCm39) M795V probably benign Het
Gm5916 A G 9: 36,039,970 (GRCm39) L6P probably damaging Het
Gpr139 A G 7: 118,744,355 (GRCm39) F77L possibly damaging Het
Kcnu1 T C 8: 26,395,976 (GRCm39) S654P possibly damaging Het
Kdm5c T A X: 151,031,762 (GRCm39) F408L probably damaging Het
Kel A G 6: 41,679,323 (GRCm39) S147P probably benign Het
Klra5 A T 6: 129,888,307 (GRCm39) probably null Het
Mastl A G 2: 23,030,010 (GRCm39) S239P probably benign Het
Med18 A T 4: 132,186,977 (GRCm39) V174D probably damaging Het
Mgat4a A T 1: 37,502,007 (GRCm39) M247K possibly damaging Het
Mx2 A C 16: 97,345,795 (GRCm39) D71A probably damaging Het
Nxt1 G T 2: 148,517,564 (GRCm39) E102* probably null Het
Or14j1 A G 17: 38,146,169 (GRCm39) Q93R possibly damaging Het
Or3a1 A G 11: 74,225,862 (GRCm39) F65S probably damaging Het
Or7g16 T C 9: 18,727,005 (GRCm39) N195S probably damaging Het
Pcdhb16 T A 18: 37,613,161 (GRCm39) V707E probably benign Het
Pdzrn4 T A 15: 92,667,768 (GRCm39) V640E probably damaging Het
Piwil4 T C 9: 14,637,282 (GRCm39) probably null Het
Pla2g4a A T 1: 149,776,950 (GRCm39) D55E probably damaging Het
Plekhg2 C A 7: 28,059,501 (GRCm39) R1276L probably damaging Het
Psd4 G A 2: 24,290,540 (GRCm39) W539* probably null Het
Rae1 G A 2: 172,845,306 (GRCm39) E33K probably damaging Het
Rbm12b1 T A 4: 12,145,563 (GRCm39) F512I probably damaging Het
Rfx6 A G 10: 51,602,952 (GRCm39) D823G possibly damaging Het
Samt3 A T X: 85,090,759 (GRCm39) Q217L probably damaging Het
Selenbp2 A G 3: 94,605,438 (GRCm39) N134S probably null Het
Selenoo T C 15: 88,984,173 (GRCm39) V663A probably damaging Het
Sp4 G T 12: 118,263,284 (GRCm39) T254N probably damaging Het
Spdya A G 17: 71,885,242 (GRCm39) K232R probably benign Het
Stom A T 2: 35,210,401 (GRCm39) V201E probably benign Het
Usp2 A G 9: 44,000,425 (GRCm39) probably benign Het
Vmn1r226 T C 17: 20,907,926 (GRCm39) S53P probably damaging Het
Vmn2r14 C T 5: 109,372,349 (GRCm39) G47D probably damaging Het
Vwf T G 6: 125,623,318 (GRCm39) L1805W probably damaging Het
Washc3 A T 10: 88,037,687 (GRCm39) Q22L probably damaging Het
Wdr81 T A 11: 75,335,546 (GRCm39) D1761V probably damaging Het
Other mutations in Sycp3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02402:Sycp3 APN 10 88,302,425 (GRCm39) intron probably benign
PIT4378001:Sycp3 UTSW 10 88,302,366 (GRCm39) nonsense probably null
R1468:Sycp3 UTSW 10 88,305,454 (GRCm39) missense possibly damaging 0.75
R1468:Sycp3 UTSW 10 88,305,454 (GRCm39) missense possibly damaging 0.75
R2857:Sycp3 UTSW 10 88,303,234 (GRCm39) missense probably damaging 1.00
R2858:Sycp3 UTSW 10 88,303,234 (GRCm39) missense probably damaging 1.00
R2897:Sycp3 UTSW 10 88,308,544 (GRCm39) missense possibly damaging 0.92
R2898:Sycp3 UTSW 10 88,308,544 (GRCm39) missense possibly damaging 0.92
R4194:Sycp3 UTSW 10 88,299,237 (GRCm39) missense probably benign 0.01
R5683:Sycp3 UTSW 10 88,308,797 (GRCm39) missense probably damaging 1.00
R6882:Sycp3 UTSW 10 88,308,791 (GRCm39) nonsense probably null
R7273:Sycp3 UTSW 10 88,305,428 (GRCm39) missense probably damaging 1.00
R7853:Sycp3 UTSW 10 88,302,368 (GRCm39) missense probably damaging 1.00
R8055:Sycp3 UTSW 10 88,298,438 (GRCm39) missense probably damaging 1.00
R8147:Sycp3 UTSW 10 88,298,467 (GRCm39) critical splice donor site probably null
R8720:Sycp3 UTSW 10 88,298,394 (GRCm39) missense probably benign 0.38
R8872:Sycp3 UTSW 10 88,302,388 (GRCm39) missense probably damaging 1.00
R9163:Sycp3 UTSW 10 88,299,734 (GRCm39) critical splice donor site probably null
Posted On 2015-04-16