Mutagenetix > Incidental Mutation

Incidental Mutation 'R3891:Syce1'

310395

Institutional Source

Beutler Lab

Gene Symbol

Syce1

Ensembl Gene

ENSMUSG00000025480

Gene Name

synaptonemal complex central element protein 1

Synonyms

4933406J07Rik

MMRRC Submission

040803-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R3891 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

140357142-140367765 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 140359809 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Phenylalanine at position 83 (L83F)

Ref Sequence

ENSEMBL: ENSMUSP00000148137 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026552] [ENSMUST00000026553] [ENSMUST00000209253] [ENSMUST00000211616]

AlphaFold

Q9D495

Predicted Effect

probably benign
Transcript: ENSMUST00000026552

SMART Domains

Protein: ENSMUSP00000026552
Gene: ENSMUSG00000025479

Domain	Start	End	E-Value	Type
transmembrane domain	2	23	N/A	INTRINSIC
Pfam:p450	33	489	1.4e-147	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000026553
AA Change: L104F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000026553
Gene: ENSMUSG00000025480
AA Change: L104F

Domain	Start	End	E-Value	Type
Pfam:SYCE1	49	200	5.5e-66	PFAM
coiled coil region	237	294	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204061

Predicted Effect

probably benign
Transcript: ENSMUST00000209253

Predicted Effect

probably damaging
Transcript: ENSMUST00000211616
AA Change: L83F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Meta Mutation Damage Score

0.1033

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.4%
20x: 95.6%

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: 49 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A3galt2	A	G	4: 128,655,847 (GRCm39)	T72A	probably damaging	Het
Ascc3	T	A	10: 50,718,289 (GRCm39)	I1994N	probably damaging	Het
C1qb	A	T	4: 136,607,727 (GRCm39)	V212E	probably damaging	Het
Cfap54	T	A	10: 92,874,708 (GRCm39)	I563F	possibly damaging	Het
Clip2	T	C	5: 134,551,847 (GRCm39)	K92E	probably damaging	Het
Clrn3	T	C	7: 135,120,194 (GRCm39)	T131A	possibly damaging	Het
Col9a1	T	C	1: 24,224,517 (GRCm39)		probably null	Het
Def8	T	C	8: 124,185,083 (GRCm39)		probably benign	Het
Diaph1	C	A	18: 38,033,691 (GRCm39)		probably benign	Het
Dmrta1	A	T	4: 89,579,831 (GRCm39)	I264F	possibly damaging	Het
Dscaml1	A	T	9: 45,628,782 (GRCm39)	D1112V	possibly damaging	Het
Ehbp1l1	A	G	19: 5,768,340 (GRCm39)	S988P	possibly damaging	Het
Gabrr2	A	G	4: 33,081,348 (GRCm39)	Y4C	probably damaging	Het
Gm10088	T	C	16: 18,847,001 (GRCm39)		noncoding transcript	Het
Gm5616	A	G	9: 48,361,809 (GRCm39)		noncoding transcript	Het
H2-T24	T	A	17: 36,326,330 (GRCm39)	I190F	possibly damaging	Het
Hmcn1	A	T	1: 150,510,946 (GRCm39)	D3592E	probably damaging	Het
Il1rap	A	G	16: 26,495,606 (GRCm39)	Y71C	probably damaging	Het
Krt1	T	A	15: 101,758,847 (GRCm39)	S106C	unknown	Het
Lsamp	T	C	16: 39,805,054 (GRCm39)	V11A	probably benign	Het
Mob1b	T	A	5: 88,901,061 (GRCm39)	I156K	probably damaging	Het
Naip2	T	A	13: 100,297,606 (GRCm39)	E810V	probably damaging	Het
Nfe2l1	A	G	11: 96,710,823 (GRCm39)	S181P	possibly damaging	Het
Nos1ap	T	C	1: 170,177,025 (GRCm39)	Y126C	probably damaging	Het
Nuak2	G	T	1: 132,259,223 (GRCm39)	A342S	possibly damaging	Het
Or10ah1-ps1	G	T	5: 143,123,152 (GRCm39)	S290R	probably benign	Het
Or2aj5	A	G	16: 19,425,205 (GRCm39)	I71T	probably damaging	Het
Or2t1	T	A	14: 14,328,114 (GRCm38)	M1K	probably null	Het
Pcdhb16	A	T	18: 37,612,422 (GRCm39)	I461F	probably benign	Het
Pcdhga10	A	C	18: 37,882,534 (GRCm39)	H765P	probably benign	Het
Pex2	C	T	3: 5,626,008 (GRCm39)	C267Y	probably damaging	Het
Pgghg	T	C	7: 140,525,616 (GRCm39)	I473T	probably damaging	Het
Polr2e	G	T	10: 79,873,213 (GRCm39)	P80T	probably benign	Het
Pum1	T	C	4: 130,491,393 (GRCm39)	L774P	probably damaging	Het
Rasef	A	G	4: 73,698,634 (GRCm39)	V9A	probably benign	Het
Rpl13	A	G	8: 123,831,907 (GRCm39)	E201G	probably damaging	Het
Skint2	A	G	4: 112,481,383 (GRCm39)	E82G	probably damaging	Het
Skor2	A	G	18: 76,946,350 (GRCm39)	D24G	unknown	Het
Slc19a3	A	T	1: 83,000,678 (GRCm39)	F113Y	probably damaging	Het
Slc29a3	T	A	10: 60,552,040 (GRCm39)	K335*	probably null	Het
Slc30a6	T	A	17: 74,726,541 (GRCm39)	D282E	probably benign	Het
Slc9a7	A	G	X: 20,052,352 (GRCm39)	F247S	probably damaging	Het
Slx4	A	T	16: 3,797,773 (GRCm39)	I1537N	probably damaging	Het
Specc1	C	T	11: 62,042,739 (GRCm39)	T872M	probably benign	Het
Stard10	G	A	7: 100,993,137 (GRCm39)	R231Q	possibly damaging	Het
Tesl1	A	G	X: 23,773,180 (GRCm39)	Y227C	probably damaging	Het
Vwa1	T	C	4: 155,857,651 (GRCm39)	E49G	probably damaging	Het
Zc3h12a	A	G	4: 125,020,678 (GRCm39)	F55S	probably damaging	Het
Zmym4	A	G	4: 126,798,269 (GRCm39)	I786T	probably benign	Het

Other mutations in Syce1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
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'- CCCTCTGAGTGCTTGCTAAG -3'
(R):5'- ACAGGAATGTGGATACCCGTAG -3'

Sequencing Primer
(F):5'- ACATATCACATCAAGTCTGTGGAC -3'
(R):5'- CGTAGGGGTAGGAACTTACCTC -3'

Posted On

2015-04-17