Mutagenetix > Incidental Mutation

Incidental Mutation 'R0608:Sycp2'

54384

Institutional Source

Beutler Lab

Gene Symbol

Sycp2

Ensembl Gene

ENSMUSG00000060445

Gene Name

synaptonemal complex protein 2

Synonyms

3830402K23Rik, 4930518F03Rik

MMRRC Submission

038797-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0608 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

178345293-178407685 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 178382404 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 396 (F396L)

Ref Sequence

ENSEMBL: ENSMUSP00000079909 (fasta)

Gene Model

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

AlphaFold

Q9CUU3

Predicted Effect

probably damaging
Transcript: ENSMUST00000081134
AA Change: F396L

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000079909
Gene: ENSMUSG00000060445
AA Change: F396L

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: 99.4%
3x: 99.0%
10x: 97.7%
20x: 95.7%

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A730017C20Rik	A	G	18: 59,062,459		probably null	Het
Akap11	A	G	14: 78,510,753	V1398A	probably benign	Het
Ampd3	C	A	7: 110,795,790	D315E	probably damaging	Het
Ampd3	T	A	7: 110,795,791	F316I	probably damaging	Het
Arhgef40	A	C	14: 51,996,974	E911D	probably damaging	Het
Atxn2l	A	G	7: 126,501,416		probably null	Het
BC117090	T	C	16: 36,323,024		probably null	Het
Bckdhb	T	G	9: 83,953,736	F98V	probably damaging	Het
Calhm1	C	T	19: 47,143,841	V112I	probably benign	Het
Ccdc28a	G	A	10: 18,224,951	R90C	probably damaging	Het
Cdc40	A	T	10: 40,848,052	Y247N	probably benign	Het
Cds1	G	A	5: 101,814,433	V305M	probably damaging	Het
Cep128	T	G	12: 90,999,535		probably benign	Het
Cep72	A	T	13: 74,038,304	H249Q	probably damaging	Het
Cfap70	A	T	14: 20,448,563	Y19N	probably damaging	Het
Col11a1	T	C	3: 114,218,715		probably benign	Het
Cysltr1	A	G	X: 106,578,655	V75A	possibly damaging	Het
Dnah17	G	T	11: 118,090,749	Y1716*	probably null	Het
Dnm1	T	C	2: 32,335,824	E383G	possibly damaging	Het
Dst	C	A	1: 34,290,356		probably null	Het
Edil3	T	C	13: 89,184,849	S375P	probably damaging	Het
Eme1	A	G	11: 94,650,082	C277R	probably damaging	Het
Enam	T	C	5: 88,493,027	W183R	possibly damaging	Het
Fbxl6	C	T	15: 76,536,753	V341M	probably benign	Het
Fgf14	A	G	14: 124,676,603	S39P	probably damaging	Het
Fmo4	C	T	1: 162,803,651	R249H	possibly damaging	Het
Gle1	T	A	2: 29,940,228	D265E	probably benign	Het
Gml2	T	C	15: 74,821,386		probably null	Het
Golgb1	G	T	16: 36,916,330	E1980*	probably null	Het
Hap1	A	G	11: 100,349,305	L555P	probably damaging	Het
Heca	T	C	10: 17,915,291	D339G	possibly damaging	Het
Hepacam2	T	C	6: 3,483,479	T101A	possibly damaging	Het
Ift88	T	C	14: 57,496,221	V707A	probably benign	Het
Kdm3a	C	T	6: 71,620,046	G252D	probably benign	Het
Klhl11	A	G	11: 100,472,242	Y163H	probably damaging	Het
Kntc1	A	T	5: 123,786,074	N1008Y	probably damaging	Het
Lrp2	G	T	2: 69,486,243	N2131K	probably benign	Het
Lrrc6	T	A	15: 66,380,474	M448L	probably benign	Het
Magi3	C	G	3: 104,017,557	G1092A	probably damaging	Het
Mef2a	G	T	7: 67,235,148	S406*	probably null	Het
Mrps26	G	T	2: 130,563,858	R27L	possibly damaging	Het
Myof	T	C	19: 37,916,504	D1624G	probably damaging	Het
Naif1	T	C	2: 32,454,896	M204T	probably benign	Het
Ndufb8	T	C	19: 44,550,345	E179G	possibly damaging	Het
Neb	A	T	2: 52,326,757	D135E	probably benign	Het
Nlrp6	C	T	7: 140,923,486	Q502*	probably null	Het
Nploc4	A	G	11: 120,413,681	L238P	probably damaging	Het
Olfr463	G	A	11: 87,893,196	H243Y	probably damaging	Het
Parp4	T	A	14: 56,602,404	V523E	probably damaging	Het
Pdgfra	T	C	5: 75,163,777	Y98H	probably damaging	Het
Plcz1	C	T	6: 139,990,733	R590H	probably damaging	Het
Pnliprp1	T	A	19: 58,738,196	Y328*	probably null	Het
Pnpla8	C	T	12: 44,283,463	P48L	probably benign	Het
Rab44	T	A	17: 29,147,343		probably null	Het
Ranbp2	T	C	10: 58,493,898	I3031T	probably damaging	Het
Rnf219	T	C	14: 104,479,527	Y470C	probably damaging	Het
Sbno1	T	C	5: 124,384,541	D1072G	probably damaging	Het
Senp7	A	G	16: 56,123,873	T187A	possibly damaging	Het
Serpinh1	A	G	7: 99,349,394	C10R	unknown	Het
Sh2d4a	A	G	8: 68,346,694	Y405C	possibly damaging	Het
Slc26a7	T	C	4: 14,621,317	D23G	probably benign	Het
Slc7a7	A	G	14: 54,377,802	L246P	probably damaging	Het
Spire1	T	C	18: 67,528,875	R163G	probably damaging	Het
Stxbp2	T	A	8: 3,632,559	D49E	probably damaging	Het
Susd2	C	T	10: 75,638,235	A509T	probably benign	Het
Syne2	T	C	12: 75,963,813	L2499P	probably damaging	Het
Syt10	C	A	15: 89,826,941	A130S	probably benign	Het
Sytl4	A	T	X: 133,962,187	D16E	probably benign	Het
Tab2	C	T	10: 7,920,119	V126I	probably damaging	Het
Tecpr1	T	C	5: 144,211,499	T363A	probably damaging	Het
Terb2	A	G	2: 122,186,335	D16G	probably benign	Het
Tm2d2	A	G	8: 25,020,536	E137G	probably benign	Het
Trim30d	T	A	7: 104,472,485	H201L	probably damaging	Het
Tspan3	A	G	9: 56,147,385		probably null	Het
Ttn	A	T	2: 76,787,323	L16268Q	probably damaging	Het
Ttn	A	T	2: 76,796,185		probably null	Het
Ubap2	T	A	4: 41,218,319	T263S	probably benign	Het
Vmn2r100	C	A	17: 19,522,120	P252Q	possibly damaging	Het
Zeb2	A	T	2: 44,996,126	M973K	possibly damaging	Het
Zfp229	A	G	17: 21,746,634	E615G	probably damaging	Het
Zfp655	T	A	5: 145,244,057	S242T	possibly damaging	Het
Zfp788	T	A	7: 41,648,281	F62I	possibly damaging	Het
Zmynd8	A	G	2: 165,787,158		probably null	Het

Other mutations in Sycp2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00484:Sycp2	APN	2	178382348	missense	probably damaging	1.00
IGL00578:Sycp2	APN	2	178350822	splice site	probably benign
IGL00646:Sycp2	APN	2	178374459	missense	probably benign	0.00
IGL01309:Sycp2	APN	2	178358111	missense	probably benign	0.15
IGL01464:Sycp2	APN	2	178401632	missense	probably damaging	0.96
IGL01539:Sycp2	APN	2	178374695	missense	probably damaging	1.00
IGL01670:Sycp2	APN	2	178378050	missense	probably benign	0.00
IGL02138:Sycp2	APN	2	178358254	missense	probably benign	0.31
IGL02138:Sycp2	APN	2	178401990	nonsense	probably null
IGL02630:Sycp2	APN	2	178401919	missense	probably damaging	1.00
IGL02673:Sycp2	APN	2	178394211	missense	possibly damaging	0.63
IGL02961:Sycp2	APN	2	178380862	missense	probably benign	0.01
IGL03084:Sycp2	APN	2	178391791	unclassified	probably benign
IGL03123:Sycp2	APN	2	178352479	nonsense	probably null
IGL03167:Sycp2	APN	2	178379498	missense	probably damaging	0.99
R0043:Sycp2	UTSW	2	178364711	missense	probably damaging	1.00
R0050:Sycp2	UTSW	2	178364711	missense	probably damaging	1.00
R0096:Sycp2	UTSW	2	178403735	missense	probably damaging	0.99
R0096:Sycp2	UTSW	2	178403735	missense	probably damaging	0.99
R0310:Sycp2	UTSW	2	178381855	missense	probably benign	0.44
R0363:Sycp2	UTSW	2	178346411	splice site	probably benign
R0456:Sycp2	UTSW	2	178381855	missense	probably benign	0.44
R0597:Sycp2	UTSW	2	178356580	missense	possibly damaging	0.54
R1112:Sycp2	UTSW	2	178352536	missense	probably benign	0.05
R1127:Sycp2	UTSW	2	178374366	missense	possibly damaging	0.72
R1208:Sycp2	UTSW	2	178356628	missense	possibly damaging	0.92
R1208:Sycp2	UTSW	2	178356628	missense	possibly damaging	0.92
R1323:Sycp2	UTSW	2	178347621	missense	possibly damaging	0.50
R1323:Sycp2	UTSW	2	178347621	missense	possibly damaging	0.50
R1413:Sycp2	UTSW	2	178347797	missense	probably benign	0.00
R1557:Sycp2	UTSW	2	178395216	unclassified	probably benign
R1562:Sycp2	UTSW	2	178382385	missense	probably damaging	1.00
R1585:Sycp2	UTSW	2	178351668	missense	possibly damaging	0.50
R1932:Sycp2	UTSW	2	178381957	missense	probably damaging	1.00
R1950:Sycp2	UTSW	2	178402800	missense	probably benign	0.00
R2001:Sycp2	UTSW	2	178378055	missense	probably benign	0.05
R2105:Sycp2	UTSW	2	178350138	splice site	probably null
R2382:Sycp2	UTSW	2	178378018	critical splice donor site	probably null
R2403:Sycp2	UTSW	2	178403735	nonsense	probably null
R2483:Sycp2	UTSW	2	178374595	missense	probably damaging	0.98
R3003:Sycp2	UTSW	2	178358123	missense	probably benign	0.01
R3418:Sycp2	UTSW	2	178401653	splice site	probably benign
R3686:Sycp2	UTSW	2	178374384	missense	probably benign	0.16
R4038:Sycp2	UTSW	2	178380927	missense	possibly damaging	0.72
R4039:Sycp2	UTSW	2	178380927	missense	possibly damaging	0.72
R4272:Sycp2	UTSW	2	178358224	missense	probably benign	0.04
R4343:Sycp2	UTSW	2	178380947	missense	probably damaging	0.99
R4491:Sycp2	UTSW	2	178374985	missense	probably damaging	1.00
R4534:Sycp2	UTSW	2	178355009	missense	probably damaging	1.00
R4720:Sycp2	UTSW	2	178374432	missense	probably benign	0.11
R4805:Sycp2	UTSW	2	178393961	unclassified	probably benign
R4807:Sycp2	UTSW	2	178393961	unclassified	probably benign
R4808:Sycp2	UTSW	2	178393961	unclassified	probably benign
R4906:Sycp2	UTSW	2	178403657	critical splice donor site	probably null
R4910:Sycp2	UTSW	2	178358224	missense	probably benign	0.04
R5282:Sycp2	UTSW	2	178403761	missense	probably damaging	1.00
R5285:Sycp2	UTSW	2	178392398	splice site	probably null
R5316:Sycp2	UTSW	2	178356503	missense	probably benign	0.00
R5389:Sycp2	UTSW	2	178377702	splice site	probably null
R5621:Sycp2	UTSW	2	178381918	missense	probably benign	0.05
R5652:Sycp2	UTSW	2	178358705	splice site	probably null
R5880:Sycp2	UTSW	2	178374470	missense	possibly damaging	0.92
R6114:Sycp2	UTSW	2	178348245	missense	probably benign	0.25
R6115:Sycp2	UTSW	2	178348245	missense	probably benign	0.25
R6186:Sycp2	UTSW	2	178383560	missense	probably damaging	0.97
R6351:Sycp2	UTSW	2	178363416	missense	probably damaging	1.00
R6509:Sycp2	UTSW	2	178395894	missense	probably damaging	1.00
R6536:Sycp2	UTSW	2	178351648	missense	probably damaging	1.00
R6679:Sycp2	UTSW	2	178380928	missense	probably damaging	0.96
R6687:Sycp2	UTSW	2	178354960	missense	probably damaging	0.99
R6761:Sycp2	UTSW	2	178374351	splice site	probably null
R6786:Sycp2	UTSW	2	178383552	missense	possibly damaging	0.63
R7357:Sycp2	UTSW	2	178403804	splice site	probably null
R7422:Sycp2	UTSW	2	178394151	missense	probably damaging	1.00
R7519:Sycp2	UTSW	2	178346333	makesense	probably null
R7805:Sycp2	UTSW	2	178380858	missense	probably damaging	0.99
R7960:Sycp2	UTSW	2	178404660	missense	probably null	0.90
R8022:Sycp2	UTSW	2	178355062	missense	probably damaging	1.00
R8037:Sycp2	UTSW	2	178403778	missense	probably damaging	1.00
R8038:Sycp2	UTSW	2	178403778	missense	probably damaging	1.00
R8039:Sycp2	UTSW	2	178374585	missense	probably benign	0.05
R8159:Sycp2	UTSW	2	178354977	missense	probably damaging	0.97
R8233:Sycp2	UTSW	2	178356634	missense	probably damaging	1.00
R8436:Sycp2	UTSW	2	178362968	missense	probably benign	0.44
R8437:Sycp2	UTSW	2	178364858	missense	probably damaging	1.00
R8528:Sycp2	UTSW	2	178374533	missense	probably damaging	1.00
R8679:Sycp2	UTSW	2	178350975	missense	probably damaging	0.99
R8711:Sycp2	UTSW	2	178348295	missense	probably benign	0.41
R8843:Sycp2	UTSW	2	178348259	missense	probably damaging	0.99
R9044:Sycp2	UTSW	2	178347824	missense	probably damaging	1.00
R9067:Sycp2	UTSW	2	178347421	critical splice donor site	probably null
R9203:Sycp2	UTSW	2	178355113	missense	probably damaging	1.00
R9263:Sycp2	UTSW	2	178394138	missense	probably damaging	1.00
R9301:Sycp2	UTSW	2	178381857	missense	probably benign	0.00
R9596:Sycp2	UTSW	2	178348419	critical splice donor site	probably null
R9633:Sycp2	UTSW	2	178356461	missense	probably damaging	1.00
R9715:Sycp2	UTSW	2	178394164	missense	probably damaging	1.00
R9748:Sycp2	UTSW	2	178383511	missense	probably damaging	1.00
Z1088:Sycp2	UTSW	2	178374367	missense	probably benign
Z1088:Sycp2	UTSW	2	178381934	missense	probably benign	0.17
Z1176:Sycp2	UTSW	2	178364881	missense	probably damaging	1.00
Z1177:Sycp2	UTSW	2	178380875	missense	probably damaging	1.00
Z1191:Sycp2	UTSW	2	178350869	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- ACCTCATCCTGGCTGCTGCTATT -3'
(R):5'- agagcctgcctcaaagaaaATTTCAAAGA -3'

Sequencing Primer
(F):5'- TGTAAGCAAATTCTGCCACTC -3'
(R):5'- GCAACCCTTGTATAGAAATCAAAATG -3'

Posted On

2013-07-11