Incidental Mutation 'R5040:Syce1'
ID 458182
Institutional Source Beutler Lab
Gene Symbol Syce1
Ensembl Gene ENSMUSG00000025480
Gene Name synaptonemal complex central element protein 1
Synonyms 4933406J07Rik
MMRRC Submission 042630-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5040 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 140357142-140367765 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 140358978 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Glutamine at position 178 (H178Q)
Ref Sequence ENSEMBL: ENSMUSP00000026553 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026552] [ENSMUST00000026553] [ENSMUST00000209253] [ENSMUST00000210235] [ENSMUST00000211616]
AlphaFold Q9D495
Predicted Effect probably benign
Transcript: ENSMUST00000026552
SMART Domains Protein: ENSMUSP00000026552
Gene: ENSMUSG00000025479

DomainStartEndE-ValueType
transmembrane domain 2 23 N/A INTRINSIC
Pfam:p450 33 489 1.4e-147 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000026553
AA Change: H178Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000026553
Gene: ENSMUSG00000025480
AA Change: H178Q

DomainStartEndE-ValueType
Pfam:SYCE1 49 200 5.5e-66 PFAM
coiled coil region 237 294 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000209253
Predicted Effect probably benign
Transcript: ENSMUST00000210235
Predicted Effect probably benign
Transcript: ENSMUST00000211616
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.2%
Validation Efficiency 98% (63/64)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the synaptonemal complex, which links homologous chromosomes during prophase I of meiosis. The tripartite structure of the complex is highly conserved amongst metazoans. It consists of two lateral elements and a central region formed by transverse elements and a central element. The protein encoded by this gene localizes to the central element and is required for initiation and elongation of the synapsis. Allelic variants of this gene have been associated with premature ovarian failure and spermatogenic failure. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]
PHENOTYPE: Mice homozygous for a null allele exhibit small ovaries and small testes, severe defects in gametogenesis, and infertility in both sexes. Meiosis is arrested, homologous chromosomes fail to synapse, and meiotic double-strand breaks are formed but are notefficiently repaired. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc6 T C 7: 45,669,578 (GRCm39) Q159R probably benign Het
Ap2a1 T C 7: 44,555,228 (GRCm39) I446V possibly damaging Het
Areg A T 5: 91,292,198 (GRCm39) H166L possibly damaging Het
Arhgap15 T C 2: 43,734,825 (GRCm39) probably null Het
Arhgef17 T C 7: 100,526,032 (GRCm39) D874G probably benign Het
Cast T C 13: 74,872,932 (GRCm39) T452A probably damaging Het
Ccdc154 A T 17: 25,383,566 (GRCm39) T208S probably benign Het
Chst11 T A 10: 83,026,780 (GRCm39) L69Q probably benign Het
Clec2d G A 6: 129,161,793 (GRCm39) R142K probably damaging Het
Dis3l2 A T 1: 86,785,059 (GRCm39) I303F probably damaging Het
Dync2h1 A G 9: 6,992,625 (GRCm39) Y3979H probably benign Het
Ehmt1 A T 2: 24,774,316 (GRCm39) C162S probably benign Het
Eif4g3 G T 4: 137,824,200 (GRCm39) M239I probably damaging Het
Eif5 A G 12: 111,506,284 (GRCm39) D41G probably damaging Het
Elapor1 T A 3: 108,382,317 (GRCm39) D284V probably damaging Het
Fat1 C T 8: 45,476,417 (GRCm39) A1821V probably damaging Het
Fry G A 5: 150,312,319 (GRCm39) A745T probably damaging Het
Galnt9 T C 5: 110,765,771 (GRCm39) L491P probably damaging Het
Gata3 A G 2: 9,863,326 (GRCm39) L396P probably damaging Het
Gyg1 A G 3: 20,176,823 (GRCm39) probably benign Het
Hhip C A 8: 80,724,235 (GRCm39) V336L probably benign Het
Hipk2 G A 6: 38,707,816 (GRCm39) P660S possibly damaging Het
Hnrnpul1 G A 7: 25,442,414 (GRCm39) T276I possibly damaging Het
Ifnl2 G T 7: 28,208,511 (GRCm39) R147S possibly damaging Het
Ilvbl A G 10: 78,419,152 (GRCm39) D467G probably damaging Het
Kcnh1 A T 1: 192,187,783 (GRCm39) H748L probably benign Het
Lyg1 A C 1: 37,989,892 (GRCm39) probably benign Het
Mak A G 13: 41,183,574 (GRCm39) Y544H possibly damaging Het
Med1 A G 11: 98,046,230 (GRCm39) probably benign Het
Mogat2 T C 7: 98,887,724 (GRCm39) T17A possibly damaging Het
Myom3 T C 4: 135,516,970 (GRCm39) S847P probably damaging Het
Nprl2 T G 9: 107,419,599 (GRCm39) C9G probably null Het
Or5b125-ps1 T A 19: 13,056,307 (GRCm39) noncoding transcript Het
Pcmtd1 T C 1: 7,190,599 (GRCm39) Y23H probably damaging Het
Pkd1 C A 17: 24,790,234 (GRCm39) H972Q probably benign Het
Rbm26 A G 14: 105,358,452 (GRCm39) I929T probably benign Het
Scrn2 A G 11: 96,921,709 (GRCm39) T60A probably damaging Het
Setdb2 A T 14: 59,653,156 (GRCm39) I398N probably damaging Het
Setx A G 2: 29,029,350 (GRCm39) E206G probably damaging Het
Sez6 T C 11: 77,859,915 (GRCm39) probably null Het
Sh3bp4 C T 1: 89,071,962 (GRCm39) S270L probably damaging Het
Stac3 T C 10: 127,343,993 (GRCm39) I297T probably damaging Het
Styxl2 G A 1: 165,927,914 (GRCm39) T566I probably benign Het
Supv3l1 A T 10: 62,282,844 (GRCm39) V139E possibly damaging Het
Tamalin G A 15: 101,126,923 (GRCm39) V134I probably damaging Het
Tcp10c T A 17: 13,588,453 (GRCm39) M344K possibly damaging Het
Tcstv7a C T 13: 120,290,025 (GRCm39) W57* probably null Het
Tmc1 A G 19: 20,801,394 (GRCm39) V502A possibly damaging Het
Tmco4 G T 4: 138,747,477 (GRCm39) G242V probably damaging Het
Trp53bp2 G A 1: 182,272,271 (GRCm39) R460H probably damaging Het
Virma T A 4: 11,528,746 (GRCm39) C1328S probably benign Het
Zfp366 A G 13: 99,364,875 (GRCm39) D12G probably damaging Het
Zfp457 C T 13: 67,440,899 (GRCm39) A463T probably benign Het
Other mutations in Syce1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02112:Syce1 APN 7 140,359,545 (GRCm39) missense probably benign
IGL03304:Syce1 APN 7 140,357,623 (GRCm39) missense possibly damaging 0.67
R0918:Syce1 UTSW 7 140,360,436 (GRCm39) missense probably damaging 1.00
R1106:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R1169:Syce1 UTSW 7 140,358,120 (GRCm39) missense probably benign 0.00
R1430:Syce1 UTSW 7 140,359,351 (GRCm39) unclassified probably benign
R1436:Syce1 UTSW 7 140,357,593 (GRCm39) missense possibly damaging 0.84
R1650:Syce1 UTSW 7 140,358,300 (GRCm39) missense possibly damaging 0.62
R2081:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R2082:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R3890:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R3891:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R4006:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R4007:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R4077:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R4078:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R4079:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R4817:Syce1 UTSW 7 140,358,336 (GRCm39) missense probably benign 0.00
R4824:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R5766:Syce1 UTSW 7 140,357,894 (GRCm39) missense probably damaging 1.00
R6380:Syce1 UTSW 7 140,358,978 (GRCm39) missense probably damaging 1.00
R7048:Syce1 UTSW 7 140,359,281 (GRCm39) missense possibly damaging 0.73
R8681:Syce1 UTSW 7 140,361,987 (GRCm39) missense possibly damaging 0.58
Y4338:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GAACACTGAATGGACACAGC -3'
(R):5'- GGTATAGTAATGCCCGGGATGG -3'

Sequencing Primer
(F):5'- CTGAATGGACACAGCAACATG -3'
(R):5'- CCATAGTCCTGGATGGTCAAG -3'
Posted On 2017-02-24