Mutagenetix > Incidental Mutation

Incidental Mutation 'R5285:Sycp2'

402970

Institutional Source

Beutler Lab

Gene Symbol

Sycp2

Ensembl Gene

ENSMUSG00000060445

Gene Name

synaptonemal complex protein 2

Synonyms

3830402K23Rik, 4930518F03Rik

MMRRC Submission

042869-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5285 (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 178034191 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000079909 (fasta)

Gene Model

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

AlphaFold

Q9CUU3

Predicted Effect

probably null
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 null
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 null
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

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.2%
20x: 95.2%

Validation Efficiency

98% (65/66)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933405L10Rik	A	G	8: 106,435,097 (GRCm39)	T12A	probably benign	Het
Acbd6	T	A	1: 155,434,471 (GRCm39)	S30T	probably benign	Het
Adcy8	G	T	15: 64,639,706 (GRCm39)	H685N	possibly damaging	Het
Aldh1l1	A	T	6: 90,553,752 (GRCm39)	K539*	probably null	Het
Ap1m2	G	T	9: 21,216,933 (GRCm39)	Y134*	probably null	Het
Apobr	A	G	7: 126,184,175 (GRCm39)		probably benign	Het
Atl1	A	G	12: 70,001,273 (GRCm39)	K345R	probably benign	Het
Avil	T	C	10: 126,854,328 (GRCm39)	L765P	probably damaging	Het
Caps2	T	A	10: 112,044,216 (GRCm39)	Y472N	probably benign	Het
Catspere2	A	G	1: 177,931,454 (GRCm39)	K458E	unknown	Het
Cd177	A	T	7: 24,445,674 (GRCm39)	S590T	probably benign	Het
Cep295	T	C	9: 15,233,887 (GRCm39)	D2223G	probably benign	Het
Cfh	T	C	1: 140,028,636 (GRCm39)	T493A	probably benign	Het
Chek1	T	C	9: 36,625,748 (GRCm39)	D299G	probably benign	Het
Cpox	G	A	16: 58,495,649 (GRCm39)	G322D	probably damaging	Het
Crhr1	A	T	11: 104,061,323 (GRCm39)	I243F	possibly damaging	Het
Cyp3a11	A	G	5: 145,791,893 (GRCm39)	V500A	probably benign	Het
Dcdc5	A	T	2: 106,198,500 (GRCm39)		noncoding transcript	Het
Ergic3	A	G	2: 155,859,957 (GRCm39)		probably benign	Het
Fabp3-ps1	T	G	10: 86,568,066 (GRCm39)		probably benign	Het
Gm6445	C	A	19: 9,585,032 (GRCm39)		noncoding transcript	Het
Gucy2d	C	A	7: 98,107,474 (GRCm39)		probably null	Het
Ighv1-19-1	C	A	12: 114,667,872 (GRCm39)		probably benign	Het
Igkv2-116	G	T	6: 68,129,463 (GRCm39)	R75L	probably benign	Het
Inhbc	C	A	10: 127,193,269 (GRCm39)	R249L	probably damaging	Het
Lrrn2	T	A	1: 132,866,983 (GRCm39)	S683T	possibly damaging	Het
Lyst	T	C	13: 13,809,011 (GRCm39)	V227A	probably benign	Het
Mroh5	TGGAG	TG	15: 73,654,923 (GRCm39)		probably benign	Het
Msh4	T	C	3: 153,579,350 (GRCm39)	N587S	probably benign	Het
Mug1	G	A	6: 121,818,066 (GRCm39)	E126K	probably benign	Het
Nav2	T	C	7: 49,197,982 (GRCm39)	S1204P	probably damaging	Het
Ncor1	A	G	11: 62,283,475 (GRCm39)	I413T	probably damaging	Het
Nipa2	A	T	7: 55,582,760 (GRCm39)	Y328*	probably null	Het
Or1e25	T	A	11: 73,493,767 (GRCm39)	Y120*	probably null	Het
Or51a24	A	G	7: 103,733,340 (GRCm39)	*316R	probably null	Het
Or52s1	C	T	7: 102,862,005 (GRCm39)	R302*	probably null	Het
Or5k15	A	T	16: 58,710,471 (GRCm39)	Y37*	probably null	Het
Or5k3	T	C	16: 58,969,633 (GRCm39)	L140P	probably damaging	Het
Pla2g4e	T	C	2: 120,019,985 (GRCm39)	D155G	probably damaging	Het
Plxnb1	C	T	9: 108,937,527 (GRCm39)	T1176I	probably damaging	Het
Polg	A	G	7: 79,114,973 (GRCm39)		probably benign	Het
Prl8a2	G	A	13: 27,534,116 (GRCm39)		probably null	Het
Prmt7	G	A	8: 106,974,991 (GRCm39)	R529Q	probably benign	Het
Psg17	T	A	7: 18,554,126 (GRCm39)	L41F	probably benign	Het
Rad18	T	C	6: 112,663,726 (GRCm39)	R73G	probably benign	Het
Rhpn2	G	T	7: 35,080,990 (GRCm39)		probably benign	Het
Robo4	CGG	CG	9: 37,322,786 (GRCm39)		probably null	Het
Sarm1	A	G	11: 78,388,265 (GRCm39)	F7S	probably benign	Het
Sgip1	T	A	4: 102,778,674 (GRCm39)		probably benign	Het
Sh3gl2	A	G	4: 85,294,686 (GRCm39)	K99R	probably benign	Het
Sorbs1	G	A	19: 40,310,334 (GRCm39)	T1018I	probably damaging	Het
Spns2	G	A	11: 72,380,305 (GRCm39)	A106V	possibly damaging	Het
Stab1	A	G	14: 30,865,433 (GRCm39)		probably benign	Het
Steap3	T	C	1: 120,169,610 (GRCm39)	D191G	probably damaging	Het
Stxbp5	T	C	10: 9,674,019 (GRCm39)		probably null	Het
Tm6sf1	A	G	7: 81,509,200 (GRCm39)	S2G	possibly damaging	Het
Usp24	T	A	4: 106,264,230 (GRCm39)	D1720E	probably benign	Het
Vmn1r200	G	A	13: 22,579,457 (GRCm39)	E78K	possibly damaging	Het
Vmn2r120	A	G	17: 57,843,703 (GRCm39)	L47P	probably damaging	Het
Vmn2r14	T	C	5: 109,365,442 (GRCm39)	N544S	probably damaging	Het
Vwa1	C	T	4: 155,855,352 (GRCm39)	A254T	probably benign	Het
Zfp7	G	A	15: 76,775,422 (GRCm39)	R488Q	probably damaging	Het
Zfp940	A	T	7: 29,545,025 (GRCm39)	L294H	probably damaging	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
R3418:Sycp2	UTSW	2	178,043,446 (GRCm39)	splice site	probably benign
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
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'- TAGCATCGTCTAAGTCTAGCAC -3'
(R):5'- TTCAAGTCCCATAGGAACTTCCATTG -3'

Sequencing Primer
(F):5'- TCCAATAGTTGAGGTTTGTAT -3'
(R):5'- TATTTGAGGCCAGCTCAGAC -3'

Posted On

2016-07-22