Mutagenetix > Incidental Mutation

Incidental Mutation 'R6114:Sycp2'

484996

Institutional Source

Beutler Lab

Gene Symbol

Sycp2

Ensembl Gene

ENSMUSG00000060445

Gene Name

synaptonemal complex protein 2

Synonyms

3830402K23Rik, 4930518F03Rik

MMRRC Submission

044263-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6114 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

177987086-178049478 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to C at 177990038 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glycine at position 1403 (R1403G)

Ref Sequence

ENSEMBL: ENSMUSP00000079909 (fasta)

Gene Model

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

AlphaFold

Q9CUU3

Predicted Effect

probably benign
Transcript: ENSMUST00000081134
AA Change: R1403G

PolyPhen 2 Score 0.255 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000079909
Gene: ENSMUSG00000060445
AA Change: R1403G

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

noncoding transcript
Transcript: ENSMUST00000132611

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.0%
20x: 94.0%

Validation Efficiency

94% (60/64)

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
Adamdec1	C	A	14: 68,809,252 (GRCm39)	V237L	probably benign	Het
Aff1	T	C	5: 103,990,163 (GRCm39)	S878P	probably damaging	Het
Ahcy	A	C	2: 154,904,079 (GRCm39)	L386R	probably damaging	Het
Ank2	T	C	3: 126,804,700 (GRCm39)	N607D	probably damaging	Het
Arid5b	T	C	10: 67,933,574 (GRCm39)	D776G	possibly damaging	Het
Art4	T	A	6: 136,834,211 (GRCm39)	T11S	unknown	Het
Blm	T	C	7: 80,163,235 (GRCm39)	T39A	probably damaging	Het
Cabin1	T	A	10: 75,583,805 (GRCm39)	M221L	probably benign	Het
Cacna1c	T	C	6: 118,573,101 (GRCm39)	T1675A	probably benign	Het
Cacnb2	A	T	2: 14,980,012 (GRCm39)	H285L	possibly damaging	Het
Cchcr1	A	G	17: 35,836,227 (GRCm39)	E339G	probably damaging	Het
Cd14	A	G	18: 36,859,006 (GRCm39)	W150R	probably damaging	Het
Cep162	A	G	9: 87,085,763 (GRCm39)	I1187T	probably benign	Het
Cntnap4	A	G	8: 113,568,385 (GRCm39)	H807R	probably damaging	Het
Copb1	T	A	7: 113,846,036 (GRCm39)	H178L	probably benign	Het
Cpxm2	A	G	7: 131,756,035 (GRCm39)	V103A	probably benign	Het
Egfr	A	G	11: 16,854,374 (GRCm39)	T849A	possibly damaging	Het
Endou	T	A	15: 97,611,757 (GRCm39)	K294*	probably null	Het
Hoxd9	A	G	2: 74,529,709 (GRCm39)	N322D	probably damaging	Het
Hsph1	C	A	5: 149,550,852 (GRCm39)	V416L	possibly damaging	Het
Igkv4-78	T	A	6: 69,036,743 (GRCm39)	T97S	possibly damaging	Het
Itga10	G	T	3: 96,556,351 (GRCm39)	C162F	probably damaging	Het
Lmod2	A	G	6: 24,603,691 (GRCm39)	E222G	probably damaging	Het
Lpar5	A	G	6: 125,058,639 (GRCm39)	N120S	probably damaging	Het
Lrrc37	T	A	11: 103,508,617 (GRCm39)		probably benign	Het
Lrrk2	A	G	15: 91,632,029 (GRCm39)	I1318V	probably benign	Het
Lst1	T	C	17: 35,407,336 (GRCm39)	T11A	possibly damaging	Het
Mfn1	C	A	3: 32,617,985 (GRCm39)	A106D	probably damaging	Het
Ms4a12	G	T	19: 11,192,654 (GRCm39)	N227K	probably benign	Het
Nr1h4	T	A	10: 89,314,678 (GRCm39)	N273Y	possibly damaging	Het
Nrdc	A	T	4: 108,901,782 (GRCm39)	K617M	probably damaging	Het
Or10a3b	A	T	7: 108,444,593 (GRCm39)	M208K	possibly damaging	Het
Or1l8	A	T	2: 36,817,701 (GRCm39)	C142S	possibly damaging	Het
Or6c202	T	A	10: 128,996,202 (GRCm39)	H217L	probably benign	Het
Pcdhgc3	C	G	18: 37,940,925 (GRCm39)	T442R	probably benign	Het
Pcnx2	T	C	8: 126,500,686 (GRCm39)	N1468S	probably damaging	Het
Pde2a	A	T	7: 101,160,319 (GRCm39)		probably null	Het
Pitx2	C	G	3: 128,998,062 (GRCm39)		probably null	Het
Reck	T	A	4: 43,922,895 (GRCm39)	I390N	probably damaging	Het
Rora	A	G	9: 69,278,605 (GRCm39)	N254S	probably benign	Het
Samd4b	A	G	7: 28,222,217 (GRCm39)		probably null	Het
Scn8a	A	G	15: 100,938,477 (GRCm39)	T1949A	probably damaging	Het
Slc22a15	A	T	3: 101,768,168 (GRCm39)	Y346*	probably null	Het
Slc24a5	A	G	2: 124,925,012 (GRCm39)	T218A	probably benign	Het
Slc38a10	G	A	11: 120,020,138 (GRCm39)	Q305*	probably null	Het
Slc45a4	G	A	15: 73,477,453 (GRCm39)	P28S	probably damaging	Het
Smyd5	A	T	6: 85,417,244 (GRCm39)		probably benign	Het
Sox8	T	C	17: 25,786,494 (GRCm39)	D403G	probably damaging	Het
Stx7	A	G	10: 24,060,883 (GRCm39)		probably null	Het
Svil	T	C	18: 5,108,639 (GRCm39)	S1522P	probably damaging	Het
Tasor2	G	A	13: 3,640,081 (GRCm39)	T352M	probably damaging	Het
Tcf25	A	T	8: 124,111,114 (GRCm39)	K192M	probably damaging	Het
Tecpr1	C	T	5: 144,141,458 (GRCm39)	G804S	possibly damaging	Het
Teddm1a	C	G	1: 153,767,614 (GRCm39)	S26C	probably damaging	Het
Usp13	C	T	3: 32,908,818 (GRCm39)	P155S	probably damaging	Het
Usp17lb	T	A	7: 104,489,571 (GRCm39)	D451V	possibly damaging	Het
Vmn1r173	A	G	7: 23,402,254 (GRCm39)	N163S	possibly damaging	Het
Vmn2r103	G	T	17: 20,032,587 (GRCm39)	C787F	probably damaging	Het
Vmn2r106	G	A	17: 20,488,638 (GRCm39)	P587L	probably benign	Het
Wdr24	C	T	17: 26,043,579 (GRCm39)	H134Y	probably benign	Het
Zbtb40	T	A	4: 136,716,002 (GRCm39)	I988F	probably damaging	Het
Zbtb47	T	A	9: 121,594,661 (GRCm39)	F540Y	probably damaging	Het
Zfp536	A	T	7: 37,179,161 (GRCm39)	I84N	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
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
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'- TTCAGAGTTCATTTGCAGCTGATG -3'
(R):5'- AACATCTGATGGCAATGACCTCTC -3'

Sequencing Primer
(F):5'- CAGCTGATGTAAGATAGAACTATGC -3'
(R):5'- TGATGGCAATGACCTCTCAAGCTC -3'

Posted On

2017-08-16