Mutagenetix > Incidental Mutation

Incidental Mutation 'R3003:Sycp2'

257357

Institutional Source

Beutler Lab

Gene Symbol

Sycp2

Ensembl Gene

ENSMUSG00000060445

Gene Name

synaptonemal complex protein 2

Synonyms

3830402K23Rik, 4930518F03Rik

MMRRC Submission

040532-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R3003 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

177987086-178049478 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 177999916 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 1020 (Y1020C)

Ref Sequence

ENSEMBL: ENSMUSP00000079909 (fasta)

Gene Model

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

AlphaFold

Q9CUU3

Predicted Effect

probably benign
Transcript: ENSMUST00000081134
AA Change: Y1020C

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000079909
Gene: ENSMUSG00000060445
AA Change: Y1020C

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

Coding Region Coverage

1x: 99.1%
3x: 98.6%
10x: 97.2%
20x: 94.9%

Validation Efficiency

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: 27 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc1	T	C	16: 14,254,393 (GRCm39)	V568A	probably damaging	Het
Acd	C	T	8: 106,426,913 (GRCm39)		probably null	Het
Acly	T	C	11: 100,395,053 (GRCm39)	K469E	possibly damaging	Het
Adh6b	G	T	3: 138,063,532 (GRCm39)	L248F	possibly damaging	Het
Atg9b	G	T	5: 24,596,217 (GRCm39)	D192E	probably damaging	Het
Ccdc180	A	G	4: 45,899,988 (GRCm39)	D182G	probably benign	Het
Cep112	A	G	11: 108,331,329 (GRCm39)	E178G	probably damaging	Het
Clptm1l	C	T	13: 73,765,875 (GRCm39)	T471I	possibly damaging	Het
Csmd1	A	G	8: 16,246,184 (GRCm39)	F1072L	probably damaging	Het
Eprs1	T	C	1: 185,156,588 (GRCm39)		probably null	Het
Il27ra	G	T	8: 84,758,660 (GRCm39)	S499*	probably null	Het
Klk1b11	T	C	7: 43,426,419 (GRCm39)	I51T	probably damaging	Het
Lct	T	C	1: 128,231,963 (GRCm39)	M629V	probably damaging	Het
Mprip	A	G	11: 59,618,381 (GRCm39)	T91A	possibly damaging	Het
Pfpl	T	C	19: 12,407,690 (GRCm39)	I647T	possibly damaging	Het
Plxnc1	A	T	10: 94,629,080 (GRCm39)	F1565I	probably damaging	Het
Prr5	G	T	15: 84,656,031 (GRCm39)	C344F	probably damaging	Het
Rnf17	T	C	14: 56,738,004 (GRCm39)	W1262R	probably damaging	Het
Rptor	G	A	11: 119,763,197 (GRCm39)	R927Q	possibly damaging	Het
Slitrk5	A	G	14: 111,917,014 (GRCm39)	K213E	probably damaging	Het
Smarcd1	C	A	15: 99,610,065 (GRCm39)	P432Q	probably damaging	Het
Stat4	A	G	1: 52,142,145 (GRCm39)	D664G	probably damaging	Het
Suz12	T	A	11: 79,910,587 (GRCm39)	W313R	probably damaging	Het
Tmem181a	T	A	17: 6,346,061 (GRCm39)	L185H	probably damaging	Het
Tmem81	A	G	1: 132,435,752 (GRCm39)	N186S	probably benign	Het
Tut4	G	A	4: 108,370,125 (GRCm39)	E714K	probably damaging	Het
Vmn2r98	A	G	17: 19,286,125 (GRCm39)	M208V	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
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
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'- CTTGAGCTTAAGATAGAACTGCTC -3'
(R):5'- GCATACGCACACACTTAAAGTTG -3'

Sequencing Primer
(F):5'- CTGCTCACAGTAATTAACCATCTAC -3'
(R):5'- CTGGTCATCTTAGATATTGCATGATG -3'

Posted On

2015-01-11