Mutagenetix > Incidental Mutation

Incidental Mutation 'R1650:Syce1'

174184

Institutional Source

Beutler Lab

Gene Symbol

Syce1

Ensembl Gene

ENSMUSG00000025480

Gene Name

synaptonemal complex central element protein 1

Synonyms

4933406J07Rik

MMRRC Submission

039686-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1650 (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 140358300 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Phenylalanine at position 216 (C216F)

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

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000026553
AA Change: C216F

PolyPhen 2 Score 0.619 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000026553
Gene: ENSMUSG00000025480
AA Change: C216F

Domain	Start	End	E-Value	Type
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

0.2248

Coding Region Coverage

1x: 98.7%
3x: 97.4%
10x: 93.0%
20x: 83.4%

Validation Efficiency

99% (86/87)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abtb2	T	G	2: 103,532,747 (GRCm39)	V515G	probably damaging	Het
Ark2c	A	C	18: 77,550,113 (GRCm39)		probably null	Het
Arl5a	A	T	2: 52,302,117 (GRCm39)	I99N	probably damaging	Het
Atp8b1	A	G	18: 64,704,620 (GRCm39)		probably benign	Het
Bag4	T	A	8: 26,267,452 (GRCm39)	Q126L	probably damaging	Het
Ccser1	A	G	6: 61,615,474 (GRCm39)	T659A	probably benign	Het
Cenpn	A	G	8: 117,661,498 (GRCm39)	D199G	probably damaging	Het
Cfhr3	A	G	1: 139,521,564 (GRCm39)		noncoding transcript	Het
Clca3a2	T	A	3: 144,797,973 (GRCm39)	H164L	probably damaging	Het
Col5a1	C	A	2: 27,812,171 (GRCm39)	S84R	unknown	Het
Ctsc	T	A	7: 87,930,634 (GRCm39)	L71*	probably null	Het
Cyp2c70	A	G	19: 40,153,921 (GRCm39)	Y223H	probably benign	Het
Dbt	A	G	3: 116,328,381 (GRCm39)		probably null	Het
Dlg2	T	C	7: 92,080,259 (GRCm39)	V614A	probably damaging	Het
Dll4	T	C	2: 119,161,611 (GRCm39)	S398P	probably damaging	Het
Dyrk4	T	C	6: 126,876,792 (GRCm39)	K62E	probably benign	Het
Fgf22	A	T	10: 79,591,023 (GRCm39)	Y24F	probably damaging	Het
Ggt5	A	G	10: 75,440,595 (GRCm39)	R239G	probably benign	Het
Gm11360	C	T	13: 28,140,379 (GRCm39)	A81V	unknown	Het
Htr5b	T	A	1: 121,455,891 (GRCm39)	T10S	probably benign	Het
Igsf10	T	C	3: 59,233,583 (GRCm39)	R1717G	probably damaging	Het
Itsn2	T	A	12: 4,687,767 (GRCm39)	V556D	probably damaging	Het
Kdm3b	T	C	18: 34,942,168 (GRCm39)	V553A	possibly damaging	Het
Krt84	G	A	15: 101,434,398 (GRCm39)	S523F	possibly damaging	Het
Lca5l	T	C	16: 95,980,140 (GRCm39)		probably null	Het
Lmbrd1	T	C	1: 24,750,639 (GRCm39)	W171R	probably damaging	Het
Lrp6	T	C	6: 134,445,732 (GRCm39)	Y1027C	probably benign	Het
Macf1	A	T	4: 123,350,393 (GRCm39)	Y1702*	probably null	Het
Mon2	T	C	10: 122,831,682 (GRCm39)	I1675V	probably benign	Het
Mtcl1	T	A	17: 66,692,871 (GRCm39)	K486M	probably damaging	Het
Nek1	A	T	8: 61,489,110 (GRCm39)	H338L	probably benign	Het
Ola1	A	T	2: 72,987,238 (GRCm39)	D131E	possibly damaging	Het
Olr1	T	A	6: 129,484,052 (GRCm39)	M7L	probably benign	Het
Or1f12	T	C	13: 21,721,249 (GRCm39)	N294D	probably damaging	Het
Or4k36	C	T	2: 111,146,640 (GRCm39)	A272V	probably benign	Het
Or5t18	A	T	2: 86,637,091 (GRCm39)	M84K	possibly damaging	Het
Or5w10	C	A	2: 87,375,772 (GRCm39)	V39L	probably benign	Het
Or7g27	T	G	9: 19,249,943 (GRCm39)	F62L	possibly damaging	Het
Or9m2	C	T	2: 87,821,145 (GRCm39)	A230V	probably benign	Het
Pan2	G	A	10: 128,153,768 (GRCm39)	E980K	probably damaging	Het
Pgm1	C	A	4: 99,819,276 (GRCm39)	Q149K	probably benign	Het
Pgm1	A	G	4: 99,819,267 (GRCm39)	K146E	possibly damaging	Het
Phlpp2	T	C	8: 110,660,587 (GRCm39)		probably benign	Het
Plekhs1	G	T	19: 56,459,474 (GRCm39)	G75C	probably damaging	Het
Plin4	G	A	17: 56,411,931 (GRCm39)	T700I	probably damaging	Het
Podxl2	G	A	6: 88,826,901 (GRCm39)	P71L	probably benign	Het
Pot1a	A	T	6: 25,745,964 (GRCm39)	V579D	probably damaging	Het
Poteg	A	G	8: 27,953,813 (GRCm39)	D318G	probably benign	Het
Ppp4r3a	A	T	12: 101,010,878 (GRCm39)	D554E	probably damaging	Het
Proser3	G	A	7: 30,239,751 (GRCm39)	A451V	probably damaging	Het
Shld2	T	A	14: 33,981,574 (GRCm39)		probably benign	Het
Strc	T	C	2: 121,211,366 (GRCm39)		probably benign	Het
Syne2	A	T	12: 75,951,033 (GRCm39)	K395*	probably null	Het
Trim28	G	A	7: 12,764,776 (GRCm39)	G831D	possibly damaging	Het
Tyw1	A	G	5: 130,317,752 (GRCm39)	I434V	possibly damaging	Het
Ubox5	G	A	2: 130,442,345 (GRCm39)	A114V	probably benign	Het
Ubqln3	C	T	7: 103,790,228 (GRCm39)	V621I	possibly damaging	Het
Unc79	A	G	12: 103,079,052 (GRCm39)	D1543G	possibly damaging	Het
Vmn2r115	ATCTTCT	ATCT	17: 23,578,962 (GRCm39)		probably benign	Het
Wrnip1	C	A	13: 32,989,362 (GRCm39)	H283Q	probably benign	Het
Zan	A	T	5: 137,392,863 (GRCm39)		probably benign	Het
Zcchc10	A	T	11: 53,218,229 (GRCm39)	K1*	probably null	Het
Zfp592	T	A	7: 80,687,848 (GRCm39)	S925T	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
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
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'- TCAGAGGAATGCCCTTTCCACAGAC -3'
(R):5'- TTTTGGACAGCAGCAAGGAGCAGC -3'

Sequencing Primer
(F):5'- CGTACTATGAGCAAGGATCTGTACC -3'
(R):5'- CTGCTCAAGGAAGGTGAGGTC -3'

Posted On

2014-04-24