Mutagenetix > Incidental Mutation

Incidental Mutation 'R3418:Sycp2'

266881

Institutional Source

Beutler Lab

Gene Symbol

Sycp2

Ensembl Gene

ENSMUSG00000060445

Gene Name

synaptonemal complex protein 2

Synonyms

3830402K23Rik, 4930518F03Rik

MMRRC Submission

040636-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R3418 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

177987086-178049478 bp(-) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

A to T at 178043446 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000116917 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000081134] [ENSMUST00000138175]

AlphaFold

Q9CUU3

Predicted Effect

probably benign
Transcript: ENSMUST00000081134

SMART Domains

Protein: ENSMUSP00000079909
Gene: ENSMUSG00000060445

Domain	Start	End	E-Value	Type
low complexity region	945	960	N/A	INTRINSIC
low complexity region	1006	1019	N/A	INTRINSIC
low complexity region	1076	1091	N/A	INTRINSIC
low complexity region	1195	1204	N/A	INTRINSIC
low complexity region	1273	1293	N/A	INTRINSIC
low complexity region	1355	1364	N/A	INTRINSIC
coiled coil region	1387	1429	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000138175

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.6%

Validation Efficiency

98% (61/62)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The synaptonemal complex is a proteinaceous structure that links homologous chromosomes during the prophase of meiosis. The protein encoded by this gene is a major component of the synaptonemal complex and may bind DNA at scaffold attachment regions. The encoded protein requires synaptonemal complex protein 3, but not 1, for inclusion in the synaptonemal complex. [provided by RefSeq, Jul 2008]
PHENOTYPE: Male mice homozygous for a knock-out allele are sterile due to lack of axial element formation and subsequent failure of chromosome synapsis in prophase I spermatocytes, while females are subfertile with a sharply reduced litter size. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5530400C23Rik	A	G	6: 133,271,082 (GRCm39)	Q42R	probably benign	Het
Acaa1a	A	G	9: 119,178,556 (GRCm39)		probably null	Het
Agbl5	T	C	5: 31,062,067 (GRCm39)	S756P	probably damaging	Het
Armc9	T	C	1: 86,122,060 (GRCm39)	L395P	probably damaging	Het
Cdc16	C	T	8: 13,819,489 (GRCm39)	Q362*	probably null	Het
Cdh5	C	T	8: 104,856,002 (GRCm39)	R312C	probably damaging	Het
Cep170b	C	T	12: 112,704,902 (GRCm39)	Q887*	probably null	Het
Chd9	T	C	8: 91,763,219 (GRCm39)	I2348T	probably damaging	Het
Clec9a	A	G	6: 129,398,001 (GRCm39)		probably benign	Het
Col6a3	T	C	1: 90,731,813 (GRCm39)	D873G	probably benign	Het
D130040H23Rik	T	C	8: 69,755,579 (GRCm39)	I328T	probably benign	Het
Dido1	G	T	2: 180,302,728 (GRCm39)	D1725E	possibly damaging	Het
Dnajb14	A	G	3: 137,598,631 (GRCm39)	D123G	probably null	Het
Dock2	A	T	11: 34,580,587 (GRCm39)	M661K	probably damaging	Het
Esam	C	T	9: 37,448,426 (GRCm39)		probably null	Het
Fam20c	A	T	5: 138,743,623 (GRCm39)	N220Y	probably damaging	Het
Fat2	G	T	11: 55,169,824 (GRCm39)	H2978Q	probably benign	Het
Fbn1	T	C	2: 125,162,846 (GRCm39)	T2147A	possibly damaging	Het
Fdft1	T	C	14: 63,394,070 (GRCm39)	T214A	probably damaging	Het
Fhl5	T	C	4: 25,211,252 (GRCm39)	S147G	probably benign	Het
Flrt2	A	G	12: 95,747,378 (GRCm39)	Y572C	probably damaging	Het
Gcat	A	T	15: 78,926,297 (GRCm39)	T56S	possibly damaging	Het
Gemin5	A	T	11: 58,047,454 (GRCm39)		probably null	Het
Gm4736	A	T	6: 132,092,640 (GRCm39)		noncoding transcript	Het
Grin2b	T	C	6: 135,820,108 (GRCm39)	N368S	probably benign	Het
Gsto1	T	C	19: 47,846,344 (GRCm39)	F64L	probably benign	Het
Gucy1a1	A	G	3: 82,013,440 (GRCm39)	S401P	probably damaging	Het
Htr1f	G	A	16: 64,746,260 (GRCm39)	P344L	probably damaging	Het
Ighv7-3	T	A	12: 114,116,919 (GRCm39)	Y81F	probably damaging	Het
Jakmip3	C	A	7: 138,619,474 (GRCm39)		probably benign	Het
Kcnj13	T	C	1: 87,314,641 (GRCm39)	T194A	probably benign	Het
Khdrbs3	T	C	15: 68,921,224 (GRCm39)		probably benign	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Lyn	A	T	4: 3,746,833 (GRCm39)	I204F	probably damaging	Het
Mbd6	C	G	10: 127,122,372 (GRCm39)	R152P	probably null	Het
Myof	A	G	19: 37,911,426 (GRCm39)	S1502P	probably damaging	Het
Myom2	T	G	8: 15,135,294 (GRCm39)	I499S	probably benign	Het
Nos2	T	A	11: 78,850,521 (GRCm39)	F1126L	possibly damaging	Het
Or3a4	G	A	11: 73,944,814 (GRCm39)	T257I	probably damaging	Het
P2ry1	T	C	3: 60,911,133 (GRCm39)	F91L	probably damaging	Het
Pcdh15	C	A	10: 74,420,054 (GRCm39)	D1166E	probably benign	Het
Pou6f1	C	A	15: 100,478,805 (GRCm39)	V368L	probably benign	Het
Ptcd3	A	T	6: 71,860,470 (GRCm39)	I579K	possibly damaging	Het
Rbm45	A	G	2: 76,209,362 (GRCm39)	E392G	probably damaging	Het
Rnf168	A	G	16: 32,118,010 (GRCm39)	N524D	probably benign	Het
Rnf222	G	T	11: 68,783,982 (GRCm39)	R183L	probably damaging	Het
Robo1	C	T	16: 72,832,805 (GRCm39)	T1526I	probably benign	Het
Sel1l	A	G	12: 91,776,776 (GRCm39)	W689R	probably damaging	Het
Serpinb13	T	C	1: 106,926,657 (GRCm39)	S218P	probably damaging	Het
Serpini1	A	G	3: 75,547,589 (GRCm39)	Y367C	probably damaging	Het
Slc13a2	A	G	11: 78,291,666 (GRCm39)	F329S	probably benign	Het
Smc2	T	C	4: 52,476,850 (GRCm39)		probably benign	Het
Tab2	G	A	10: 7,783,245 (GRCm39)	P679L	probably damaging	Het
Tdrd1	T	A	19: 56,819,663 (GRCm39)	N54K	possibly damaging	Het
Tgfbr2	T	C	9: 115,958,901 (GRCm39)	Y146C	probably damaging	Het
Tnfrsf11a	A	G	1: 105,737,130 (GRCm39)	D79G	possibly damaging	Het
Trpa1	T	C	1: 14,944,605 (GRCm39)	I1046M	probably benign	Het
Ubn1	A	G	16: 4,892,243 (GRCm39)		probably benign	Het
Ubp1	T	C	9: 113,780,754 (GRCm39)		probably null	Het
Vmn2r2	A	T	3: 64,024,320 (GRCm39)	F754I	probably benign	Het

Other mutations in Sycp2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00484:Sycp2	APN	2	178,024,141 (GRCm39)	missense	probably damaging	1.00
IGL00578:Sycp2	APN	2	177,992,615 (GRCm39)	splice site	probably benign
IGL00646:Sycp2	APN	2	178,016,252 (GRCm39)	missense	probably benign	0.00
IGL01309:Sycp2	APN	2	177,999,904 (GRCm39)	missense	probably benign	0.15
IGL01464:Sycp2	APN	2	178,043,425 (GRCm39)	missense	probably damaging	0.96
IGL01539:Sycp2	APN	2	178,016,488 (GRCm39)	missense	probably damaging	1.00
IGL01670:Sycp2	APN	2	178,019,843 (GRCm39)	missense	probably benign	0.00
IGL02138:Sycp2	APN	2	178,043,783 (GRCm39)	nonsense	probably null
IGL02138:Sycp2	APN	2	178,000,047 (GRCm39)	missense	probably benign	0.31
IGL02630:Sycp2	APN	2	178,043,712 (GRCm39)	missense	probably damaging	1.00
IGL02673:Sycp2	APN	2	178,036,004 (GRCm39)	missense	possibly damaging	0.63
IGL02961:Sycp2	APN	2	178,022,655 (GRCm39)	missense	probably benign	0.01
IGL03084:Sycp2	APN	2	178,033,584 (GRCm39)	unclassified	probably benign
IGL03123:Sycp2	APN	2	177,994,272 (GRCm39)	nonsense	probably null
IGL03167:Sycp2	APN	2	178,021,291 (GRCm39)	missense	probably damaging	0.99
R0043:Sycp2	UTSW	2	178,006,504 (GRCm39)	missense	probably damaging	1.00
R0050:Sycp2	UTSW	2	178,006,504 (GRCm39)	missense	probably damaging	1.00
R0096:Sycp2	UTSW	2	178,045,528 (GRCm39)	missense	probably damaging	0.99
R0096:Sycp2	UTSW	2	178,045,528 (GRCm39)	missense	probably damaging	0.99
R0310:Sycp2	UTSW	2	178,023,648 (GRCm39)	missense	probably benign	0.44
R0363:Sycp2	UTSW	2	177,988,204 (GRCm39)	splice site	probably benign
R0456:Sycp2	UTSW	2	178,023,648 (GRCm39)	missense	probably benign	0.44
R0597:Sycp2	UTSW	2	177,998,373 (GRCm39)	missense	possibly damaging	0.54
R0608:Sycp2	UTSW	2	178,024,197 (GRCm39)	missense	probably damaging	0.98
R1112:Sycp2	UTSW	2	177,994,329 (GRCm39)	missense	probably benign	0.05
R1127:Sycp2	UTSW	2	178,016,159 (GRCm39)	missense	possibly damaging	0.72
R1208:Sycp2	UTSW	2	177,998,421 (GRCm39)	missense	possibly damaging	0.92
R1208:Sycp2	UTSW	2	177,998,421 (GRCm39)	missense	possibly damaging	0.92
R1323:Sycp2	UTSW	2	177,989,414 (GRCm39)	missense	possibly damaging	0.50
R1323:Sycp2	UTSW	2	177,989,414 (GRCm39)	missense	possibly damaging	0.50
R1413:Sycp2	UTSW	2	177,989,590 (GRCm39)	missense	probably benign	0.00
R1557:Sycp2	UTSW	2	178,037,009 (GRCm39)	unclassified	probably benign
R1562:Sycp2	UTSW	2	178,024,178 (GRCm39)	missense	probably damaging	1.00
R1585:Sycp2	UTSW	2	177,993,461 (GRCm39)	missense	possibly damaging	0.50
R1932:Sycp2	UTSW	2	178,023,750 (GRCm39)	missense	probably damaging	1.00
R1950:Sycp2	UTSW	2	178,044,593 (GRCm39)	missense	probably benign	0.00
R2001:Sycp2	UTSW	2	178,019,848 (GRCm39)	missense	probably benign	0.05
R2105:Sycp2	UTSW	2	177,991,931 (GRCm39)	splice site	probably null
R2382:Sycp2	UTSW	2	178,019,811 (GRCm39)	critical splice donor site	probably null
R2403:Sycp2	UTSW	2	178,045,528 (GRCm39)	nonsense	probably null
R2483:Sycp2	UTSW	2	178,016,388 (GRCm39)	missense	probably damaging	0.98
R3003:Sycp2	UTSW	2	177,999,916 (GRCm39)	missense	probably benign	0.01
R3686:Sycp2	UTSW	2	178,016,177 (GRCm39)	missense	probably benign	0.16
R4038:Sycp2	UTSW	2	178,022,720 (GRCm39)	missense	possibly damaging	0.72
R4039:Sycp2	UTSW	2	178,022,720 (GRCm39)	missense	possibly damaging	0.72
R4272:Sycp2	UTSW	2	178,000,017 (GRCm39)	missense	probably benign	0.04
R4343:Sycp2	UTSW	2	178,022,740 (GRCm39)	missense	probably damaging	0.99
R4491:Sycp2	UTSW	2	178,016,778 (GRCm39)	missense	probably damaging	1.00
R4534:Sycp2	UTSW	2	177,996,802 (GRCm39)	missense	probably damaging	1.00
R4720:Sycp2	UTSW	2	178,016,225 (GRCm39)	missense	probably benign	0.11
R4805:Sycp2	UTSW	2	178,035,754 (GRCm39)	unclassified	probably benign
R4807:Sycp2	UTSW	2	178,035,754 (GRCm39)	unclassified	probably benign
R4808:Sycp2	UTSW	2	178,035,754 (GRCm39)	unclassified	probably benign
R4906:Sycp2	UTSW	2	178,045,450 (GRCm39)	critical splice donor site	probably null
R4910:Sycp2	UTSW	2	178,000,017 (GRCm39)	missense	probably benign	0.04
R5282:Sycp2	UTSW	2	178,045,554 (GRCm39)	missense	probably damaging	1.00
R5285:Sycp2	UTSW	2	178,034,191 (GRCm39)	splice site	probably null
R5316:Sycp2	UTSW	2	177,998,296 (GRCm39)	missense	probably benign	0.00
R5389:Sycp2	UTSW	2	178,019,495 (GRCm39)	splice site	probably null
R5621:Sycp2	UTSW	2	178,023,711 (GRCm39)	missense	probably benign	0.05
R5652:Sycp2	UTSW	2	178,000,498 (GRCm39)	splice site	probably null
R5880:Sycp2	UTSW	2	178,016,263 (GRCm39)	missense	possibly damaging	0.92
R6114:Sycp2	UTSW	2	177,990,038 (GRCm39)	missense	probably benign	0.25
R6115:Sycp2	UTSW	2	177,990,038 (GRCm39)	missense	probably benign	0.25
R6186:Sycp2	UTSW	2	178,025,353 (GRCm39)	missense	probably damaging	0.97
R6351:Sycp2	UTSW	2	178,005,209 (GRCm39)	missense	probably damaging	1.00
R6509:Sycp2	UTSW	2	178,037,687 (GRCm39)	missense	probably damaging	1.00
R6536:Sycp2	UTSW	2	177,993,441 (GRCm39)	missense	probably damaging	1.00
R6679:Sycp2	UTSW	2	178,022,721 (GRCm39)	missense	probably damaging	0.96
R6687:Sycp2	UTSW	2	177,996,753 (GRCm39)	missense	probably damaging	0.99
R6761:Sycp2	UTSW	2	178,016,144 (GRCm39)	splice site	probably null
R6786:Sycp2	UTSW	2	178,025,345 (GRCm39)	missense	possibly damaging	0.63
R7357:Sycp2	UTSW	2	178,045,597 (GRCm39)	splice site	probably null
R7422:Sycp2	UTSW	2	178,035,944 (GRCm39)	missense	probably damaging	1.00
R7519:Sycp2	UTSW	2	177,988,126 (GRCm39)	makesense	probably null
R7805:Sycp2	UTSW	2	178,022,651 (GRCm39)	missense	probably damaging	0.99
R7960:Sycp2	UTSW	2	178,046,453 (GRCm39)	missense	probably null	0.90
R8022:Sycp2	UTSW	2	177,996,855 (GRCm39)	missense	probably damaging	1.00
R8037:Sycp2	UTSW	2	178,045,571 (GRCm39)	missense	probably damaging	1.00
R8038:Sycp2	UTSW	2	178,045,571 (GRCm39)	missense	probably damaging	1.00
R8039:Sycp2	UTSW	2	178,016,378 (GRCm39)	missense	probably benign	0.05
R8159:Sycp2	UTSW	2	177,996,770 (GRCm39)	missense	probably damaging	0.97
R8233:Sycp2	UTSW	2	177,998,427 (GRCm39)	missense	probably damaging	1.00
R8436:Sycp2	UTSW	2	178,004,761 (GRCm39)	missense	probably benign	0.44
R8437:Sycp2	UTSW	2	178,006,651 (GRCm39)	missense	probably damaging	1.00
R8528:Sycp2	UTSW	2	178,016,326 (GRCm39)	missense	probably damaging	1.00
R8679:Sycp2	UTSW	2	177,992,768 (GRCm39)	missense	probably damaging	0.99
R8711:Sycp2	UTSW	2	177,990,088 (GRCm39)	missense	probably benign	0.41
R8843:Sycp2	UTSW	2	177,990,052 (GRCm39)	missense	probably damaging	0.99
R9044:Sycp2	UTSW	2	177,989,617 (GRCm39)	missense	probably damaging	1.00
R9067:Sycp2	UTSW	2	177,989,214 (GRCm39)	critical splice donor site	probably null
R9203:Sycp2	UTSW	2	177,996,906 (GRCm39)	missense	probably damaging	1.00
R9263:Sycp2	UTSW	2	178,035,931 (GRCm39)	missense	probably damaging	1.00
R9301:Sycp2	UTSW	2	178,023,650 (GRCm39)	missense	probably benign	0.00
R9596:Sycp2	UTSW	2	177,990,212 (GRCm39)	critical splice donor site	probably null
R9633:Sycp2	UTSW	2	177,998,254 (GRCm39)	missense	probably damaging	1.00
R9715:Sycp2	UTSW	2	178,035,957 (GRCm39)	missense	probably damaging	1.00
R9748:Sycp2	UTSW	2	178,025,304 (GRCm39)	missense	probably damaging	1.00
Z1088:Sycp2	UTSW	2	178,023,727 (GRCm39)	missense	probably benign	0.17
Z1088:Sycp2	UTSW	2	178,016,160 (GRCm39)	missense	probably benign
Z1176:Sycp2	UTSW	2	178,006,674 (GRCm39)	missense	probably damaging	1.00
Z1177:Sycp2	UTSW	2	178,022,668 (GRCm39)	missense	probably damaging	1.00
Z1191:Sycp2	UTSW	2	177,992,662 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- TCTGCCTCATTAACAAGTCCAC -3'
(R):5'- GGCATTGACTGTTATATAGAGCATG -3'

Sequencing Primer
(F):5'- TGAAATACCAAACTAATATCTGCCTG -3'
(R):5'- GGATTGATCTATCCAGACTGT -3'

Posted On

2015-02-18