Mutagenetix > Incidental Mutation

Incidental Mutation 'R6679:Sycp2'

527376

Institutional Source

Beutler Lab

Gene Symbol

Sycp2

Ensembl Gene

ENSMUSG00000060445

Gene Name

synaptonemal complex protein 2

Synonyms

3830402K23Rik, 4930518F03Rik

MMRRC Submission

044798-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6679 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

177987086-178049478 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 178022721 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Threonine at position 470 (M470T)

Ref Sequence

ENSEMBL: ENSMUSP00000079909 (fasta)

Gene Model

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

AlphaFold

Q9CUU3

Predicted Effect

probably damaging
Transcript: ENSMUST00000081134
AA Change: M470T

PolyPhen 2 Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000079909
Gene: ENSMUSG00000060445
AA Change: M470T

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

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 94.9%

Validation Efficiency

91% (40/44)

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: 44 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930449I24Rik	T	A	5: 146,441,750 (GRCm39)	V299E	probably damaging	Het
Adgrb3	T	C	1: 25,170,377 (GRCm39)	I767V	probably benign	Het
Ahnak2	G	A	12: 112,739,410 (GRCm39)	T748I	probably damaging	Het
Aoc3	T	A	11: 101,222,279 (GRCm39)	L129M	probably damaging	Het
Arhgef7	T	A	8: 11,874,667 (GRCm39)	M540K	possibly damaging	Het
Bod1l	T	A	5: 41,974,009 (GRCm39)	K2435M	probably damaging	Het
Col11a1	A	G	3: 113,946,368 (GRCm39)		probably null	Het
Col5a3	C	T	9: 20,690,329 (GRCm39)	G1162R	probably damaging	Het
Creb5	G	T	6: 53,662,454 (GRCm39)	M250I	possibly damaging	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Homo
Dock10	A	G	1: 80,544,514 (GRCm39)	I557T	probably benign	Het
Efcab2	G	A	1: 178,264,969 (GRCm39)	A12T	probably benign	Het
Ehd1	A	G	19: 6,344,474 (GRCm39)	N245D	probably benign	Het
Erich3	T	A	3: 154,468,066 (GRCm39)	D839E	possibly damaging	Het
Fam13b	T	C	18: 34,620,075 (GRCm39)	T270A	possibly damaging	Het
Fat2	A	T	11: 55,200,131 (GRCm39)	L981Q	probably damaging	Het
Fgfrl1	G	A	5: 108,852,838 (GRCm39)	W89*	probably null	Het
Fgfrl1	G	T	5: 108,852,839 (GRCm39)	W89C	probably damaging	Het
Gm10770	G	A	2: 150,021,569 (GRCm39)	P11S	probably damaging	Het
Gm10801	TC	TCGGC	2: 98,494,151 (GRCm39)		probably benign	Het
Hdac3	A	G	18: 38,077,986 (GRCm39)	V190A	possibly damaging	Het
Htr1a	A	G	13: 105,581,936 (GRCm39)	N392S	probably damaging	Het
Ift43	A	G	12: 86,185,592 (GRCm39)	M59V	probably benign	Het
Jakmip2	T	C	18: 43,699,014 (GRCm39)	T482A	probably damaging	Het
Myo1c	C	T	11: 75,562,461 (GRCm39)	P918S	probably benign	Het
Nme8	A	T	13: 19,875,140 (GRCm39)		probably null	Het
Or5h26	A	G	16: 58,988,209 (GRCm39)	I99T	probably benign	Het
Peg10	CCAACAACAACAACAACAACAACA	CCAACAACAACAACAACAACA	6: 4,754,276 (GRCm39)		probably benign	Het
Plec	A	G	15: 76,058,015 (GRCm39)	F3996S	probably damaging	Het
Ppfia4	A	T	1: 134,237,417 (GRCm39)	Y961N	probably damaging	Het
Rag1	G	A	2: 101,474,629 (GRCm39)	P171L	probably damaging	Het
Rbm24	A	T	13: 46,572,468 (GRCm39)		probably benign	Het
Rsf1	A	AAGGCGACGG	7: 97,229,111 (GRCm39)		probably null	Het
Rxfp3	T	C	15: 11,035,956 (GRCm39)	Y472C	probably damaging	Het
Sash1	T	A	10: 8,615,949 (GRCm39)	I638F	probably damaging	Het
Sh3glb2	G	A	2: 30,240,631 (GRCm39)	R145W	probably damaging	Het
Ston2	G	T	12: 91,614,870 (GRCm39)	P513T	probably damaging	Het
Syt10	C	A	15: 89,698,574 (GRCm39)	D257Y	probably damaging	Het
Tcfl5	G	T	2: 180,277,055 (GRCm39)	L447I	probably damaging	Het
Tlr11	T	C	14: 50,600,311 (GRCm39)	W766R	probably benign	Het
Usp33	T	A	3: 152,074,124 (GRCm39)	D19E	possibly damaging	Het
Vmn1r123	T	A	7: 20,896,868 (GRCm39)	Y253*	probably null	Het
Wdr55	G	A	18: 36,896,177 (GRCm39)	G289D	probably damaging	Het
Zfp523	C	T	17: 28,421,194 (GRCm39)	T235M	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
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
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'- GATGCCTCCTGCTTAATTCATG -3'
(R):5'- CAGCCATGAAGATGACATCATTTC -3'

Sequencing Primer
(F):5'- GCCTCCTGCTTAATTCATGATAAAC -3'
(R):5'- TGAAGATGACATCATTTCAATTAGCC -3'

Posted On

2018-07-23