Incidental Mutation 'R6380:Syce1'
ID 515270
Institutional Source Beutler Lab
Gene Symbol Syce1
Ensembl Gene ENSMUSG00000025480
Gene Name synaptonemal complex central element protein 1
Synonyms 4933406J07Rik
MMRRC Submission 044529-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6380 (G1)
Quality Score 225.009
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: 100.0%
  • 3x: 99.9%
  • 10x: 99.1%
  • 20x: 96.5%
Validation Efficiency 100% (51/51)
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: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930590J08Rik G A 6: 91,900,118 (GRCm39) G424D probably damaging Het
Aco1 T C 4: 40,185,028 (GRCm39) V566A probably benign Het
Adat1 G T 8: 112,704,704 (GRCm39) T414K probably benign Het
Alox12e A G 11: 70,211,927 (GRCm39) V194A probably benign Het
Anpep A G 7: 79,491,644 (GRCm39) V119A probably benign Het
Atat1 C A 17: 36,219,849 (GRCm39) probably null Het
Atp10a G A 7: 58,469,432 (GRCm39) W1094* probably null Het
Bcl11b T C 12: 107,969,360 (GRCm39) R15G probably benign Het
Bltp1 A G 3: 37,087,456 (GRCm39) D4019G probably benign Het
Btnl1 A G 17: 34,598,468 (GRCm39) E28G probably benign Het
Ccnd1 A G 7: 144,493,306 (GRCm39) V42A probably benign Het
Cdyl2 T A 8: 117,309,923 (GRCm39) K344N probably damaging Het
Cep68 A G 11: 20,180,498 (GRCm39) M711T probably benign Het
Cyp2j7 A G 4: 96,118,211 (GRCm39) probably null Het
Cyp3a25 A T 5: 145,935,357 (GRCm39) D86E probably damaging Het
Dclk1 G T 3: 55,154,615 (GRCm39) R15L probably damaging Het
Dpy19l1 T A 9: 24,393,341 (GRCm39) K143* probably null Het
Duox2 A G 2: 122,111,483 (GRCm39) V1405A probably benign Het
Filip1 T C 9: 79,726,906 (GRCm39) E571G probably damaging Het
Gpat2 G C 2: 127,273,838 (GRCm39) G294R possibly damaging Het
Jph1 T C 1: 17,162,071 (GRCm39) N197S probably damaging Het
Kcnt2 T C 1: 140,437,322 (GRCm39) L535S probably damaging Het
Lepr C A 4: 101,622,151 (GRCm39) S361* probably null Het
Lfng T A 5: 140,600,151 (GRCm39) probably null Het
Lpcat2 G A 8: 93,613,209 (GRCm39) A250T probably benign Het
Mab21l4 G A 1: 93,088,613 (GRCm39) probably null Het
Map3k4 A T 17: 12,490,954 (GRCm39) M159K possibly damaging Het
Notch3 A T 17: 32,363,533 (GRCm39) C1177S probably damaging Het
Olfml2b C T 1: 170,496,800 (GRCm39) P477L probably benign Het
Or51a5 A T 7: 102,771,136 (GRCm39) F281Y probably benign Het
Or5k16 T A 16: 58,736,627 (GRCm39) I126L probably damaging Het
Or6c33 A T 10: 129,853,782 (GRCm39) H184L probably benign Het
Pald1 G T 10: 61,186,714 (GRCm39) F146L possibly damaging Het
Pcdhga1 A G 18: 37,796,022 (GRCm39) D342G probably damaging Het
Plcb2 T C 2: 118,545,949 (GRCm39) S579G probably damaging Het
Prdm16 A T 4: 154,425,824 (GRCm39) S654T probably benign Het
Rab3gap2 C A 1: 184,968,181 (GRCm39) L178I probably damaging Het
Rbfox1 C T 16: 7,042,214 (GRCm39) Q23* probably null Het
Slc14a2 T G 18: 78,190,190 (GRCm39) T920P probably benign Het
Slc17a6 G A 7: 51,317,211 (GRCm39) V411M probably benign Het
Stard6 G A 18: 70,609,459 (GRCm39) V33I probably benign Het
Syne2 T A 12: 76,151,754 (GRCm39) F1872I probably damaging Het
Tor1aip1 T C 1: 155,894,234 (GRCm39) E274G possibly damaging Het
Trpm1 A T 7: 63,918,045 (GRCm39) T462S probably benign Het
Ugt3a1 C T 15: 9,306,541 (GRCm39) A230V probably benign Het
Vmn1r178 A G 7: 23,592,984 (GRCm39) T11A possibly damaging Het
Vmn2r69 A T 7: 85,061,067 (GRCm39) N172K probably benign Het
Whrn G T 4: 63,336,829 (GRCm39) P136T possibly damaging Het
Zfhx4 A G 3: 5,478,170 (GRCm39) N3570S probably damaging Het
Zfp689 A G 7: 127,043,968 (GRCm39) S221P probably damaging 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
R5040:Syce1 UTSW 7 140,358,978 (GRCm39) missense probably damaging 1.00
R5766:Syce1 UTSW 7 140,357,894 (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'- TAGGTATAGTAATGCCCGGGATG -3'

Sequencing Primer
(F):5'- CTGAATGGACACAGCAACATG -3'
(R):5'- CCATAGTCCTGGATGGTCAAG -3'
Posted On 2018-05-04