Mutagenetix > Incidental Mutation

Incidental Mutation 'PIT4378001:Sycp3'

555007

Institutional Source

Beutler Lab

Gene Symbol

Sycp3

Ensembl Gene

ENSMUSG00000020059

Gene Name

synaptonemal complex protein 3

Synonyms

Scp3, Cor1

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.117) question?

Stock #

PIT4378001 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

88295449-88309098 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

A to T at 88302366 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Stop codon at position 119 (K119*)

Ref Sequence

ENSEMBL: ENSMUSP00000020252 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020252] [ENSMUST00000117440] [ENSMUST00000123244] [ENSMUST00000125612] [ENSMUST00000148899]

AlphaFold

no structure available at present

Predicted Effect

probably null
Transcript: ENSMUST00000020252
AA Change: K119*

SMART Domains

Protein: ENSMUSP00000020252
Gene: ENSMUSG00000020059
AA Change: K119*

Domain	Start	End	E-Value	Type
low complexity region	42	53	N/A	INTRINSIC
Pfam:Cor1	101	229	6.1e-57	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000117440

SMART Domains

Protein: ENSMUSP00000112708
Gene: ENSMUSG00000060002

Domain	Start	End	E-Value	Type
low complexity region	2	12	N/A	INTRINSIC
Pfam:CDP-OH_P_transf	61	136	8.8e-18	PFAM
transmembrane domain	159	181	N/A	INTRINSIC
transmembrane domain	191	213	N/A	INTRINSIC
transmembrane domain	226	248	N/A	INTRINSIC
transmembrane domain	263	282	N/A	INTRINSIC
transmembrane domain	295	317	N/A	INTRINSIC
transmembrane domain	349	371	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000123244

SMART Domains

Protein: ENSMUSP00000137704
Gene: ENSMUSG00000020059

Domain	Start	End	E-Value	Type
low complexity region	42	53	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000125612
AA Change: K119*

SMART Domains

Protein: ENSMUSP00000137800
Gene: ENSMUSG00000020059
AA Change: K119*

Domain	Start	End	E-Value	Type
low complexity region	42	53	N/A	INTRINSIC
Pfam:Cor1	100	229	7.6e-60	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000134318

SMART Domains

Protein: ENSMUSP00000122428
Gene: ENSMUSG00000060002

Domain	Start	End	E-Value	Type
transmembrane domain	20	42	N/A	INTRINSIC
transmembrane domain	55	77	N/A	INTRINSIC
transmembrane domain	109	131	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000148899

SMART Domains

Protein: ENSMUSP00000120167
Gene: ENSMUSG00000060002

Domain	Start	End	E-Value	Type
transmembrane domain	25	47	N/A	INTRINSIC

Coding Region Coverage

1x: 93.1%
3x: 90.8%
10x: 85.0%
20x: 72.2%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an essential structural component of the synaptonemal complex. This complex is involved in synapsis, recombination and segregation of meiotic chromosomes. Mutations in this gene are associated with azoospermia in males and susceptibility to pregnancy loss in females. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, May 2010]
PHENOTYPE: Homozygous mutants are male infertile and female sub-fertile. Reduced litter size in females is due to achiasmatic oocytes, resulting in aneuploidy and embryonic death. Meiosis in males blocks at early prophase with lack of synaptonemal complexes. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310033P09Rik	T	C	11: 59,099,802 (GRCm39)	V100A	probably benign	Het
Adamtsl1	T	C	4: 86,117,601 (GRCm39)	V188A	possibly damaging	Het
Aldh6a1	T	C	12: 84,488,646 (GRCm39)	D80G	probably benign	Het
Ankrd50	T	C	3: 38,509,412 (GRCm39)	Q62R	possibly damaging	Het
Aopep	T	C	13: 63,163,021 (GRCm39)	L14P	probably damaging	Het
Arrdc1	T	A	2: 24,816,645 (GRCm39)	Y177F	probably damaging	Het
Asap1	C	T	15: 64,007,697 (GRCm39)	R384Q	probably damaging	Het
Atxn2l	A	T	7: 126,096,443 (GRCm39)	V433D	probably benign	Het
Bbs1	G	A	19: 4,941,703 (GRCm39)	A529V	probably benign	Het
Bbx	G	A	16: 50,100,836 (GRCm39)	R20*	probably null	Het
Bend5	T	C	4: 111,288,304 (GRCm39)	V106A	probably benign	Het
C1galt1	A	G	6: 7,863,944 (GRCm39)	N8S	probably benign	Het
Cdc42ep1	G	A	15: 78,733,880 (GRCm39)	D327N	possibly damaging	Het
Cep162	A	G	9: 87,099,198 (GRCm39)	S767P	probably benign	Het
Cep43	T	C	17: 8,401,105 (GRCm39)	S209P	probably damaging	Het
Csmd1	T	C	8: 15,945,728 (GRCm39)	T3562A	probably damaging	Het
Dnah7a	A	G	1: 53,570,362 (GRCm39)	S1815P	probably damaging	Het
Ei24	A	T	9: 36,697,320 (GRCm39)	L136Q	probably damaging	Het
Extl2	T	G	3: 115,804,339 (GRCm39)	M1R	probably null	Het
Fat3	T	C	9: 16,288,104 (GRCm39)	E473G	probably benign	Het
Fcgbpl1	G	A	7: 27,853,889 (GRCm39)	D1618N	possibly damaging	Het
Fhip1a	A	G	3: 85,637,858 (GRCm39)	L147P	probably damaging	Het
G6pc3	T	A	11: 102,080,827 (GRCm39)	W26R	probably damaging	Het
Hc	T	A	2: 34,921,876 (GRCm39)	Y610F	probably benign	Het
Hecw1	T	C	13: 14,552,368 (GRCm39)	D77G	probably damaging	Het
Hgf	T	C	5: 16,816,860 (GRCm39)	V497A	probably damaging	Het
Hjurp	CTCTGGGAGGGCTTGCTCCGGGGGCAGTGTGTCCTGTTCTTGTGCAGCCCCT	C	1: 88,193,999 (GRCm39)		probably benign	Het
Hyou1	A	C	9: 44,302,148 (GRCm39)	D968A	probably benign	Het
Jmjd1c	T	A	10: 67,065,692 (GRCm39)	S1525T	probably damaging	Het
Kcnc4	G	A	3: 107,354,879 (GRCm39)	T523I	probably benign	Het
Kcng1	C	T	2: 168,104,604 (GRCm39)	C414Y	probably damaging	Het
Klhdc10	T	C	6: 30,447,411 (GRCm39)	I204T	probably damaging	Het
Krt18	A	T	15: 101,938,358 (GRCm39)	T194S	probably benign	Het
Krt76	A	C	15: 101,800,842 (GRCm39)	N151K	probably damaging	Het
Krtap31-2	A	G	11: 99,827,542 (GRCm39)	T125A	possibly damaging	Het
Lama5	A	G	2: 179,831,238 (GRCm39)	V1807A	possibly damaging	Het
Lats1	T	G	10: 7,581,369 (GRCm39)	V718G	probably damaging	Het
Mef2b	A	G	8: 70,616,910 (GRCm39)	K4E	probably damaging	Het
Mertk	T	C	2: 128,624,537 (GRCm39)		probably null	Het
Mroh8	A	G	2: 157,070,620 (GRCm39)	V577A	possibly damaging	Het
Mtcl1	T	G	17: 66,745,274 (GRCm39)	N381T	probably damaging	Het
Nfyc	T	A	4: 120,647,688 (GRCm39)		probably null	Het
Nol4	C	A	18: 23,172,933 (GRCm39)	W56L	probably damaging	Het
Notch2	A	T	3: 98,050,272 (GRCm39)	D1849V	probably damaging	Het
Or10ad1	G	A	15: 98,105,452 (GRCm39)	T271I	probably damaging	Het
Or10j7	T	C	1: 173,011,381 (GRCm39)	T207A	probably benign	Het
Or14c45	A	T	7: 86,176,306 (GRCm39)	T114S	possibly damaging	Het
Or4n4b	T	C	14: 50,536,355 (GRCm39)	N137S	probably benign	Het
Or5an10	A	G	19: 12,276,076 (GRCm39)	M140T	probably damaging	Het
Or7g28	T	A	9: 19,272,471 (GRCm39)	Y60F	probably damaging	Het
Or8s5	A	G	15: 98,238,153 (GRCm39)	V239A	possibly damaging	Het
Oxr1	G	A	15: 41,664,978 (GRCm39)	V138I	probably benign	Het
Pars2	A	G	4: 106,511,490 (GRCm39)	E424G	possibly damaging	Het
Peli2	C	A	14: 48,405,726 (GRCm39)	Y50*	probably null	Het
Plag1	T	A	4: 3,905,492 (GRCm39)	H66L	probably benign	Het
Psme4	T	C	11: 30,771,079 (GRCm39)		probably benign	Het
Robo1	A	T	16: 72,801,423 (GRCm39)	S1016C	probably damaging	Het
Rrbp1	A	G	2: 143,816,460 (GRCm39)	V723A	probably benign	Het
Sgip1	C	A	4: 102,778,280 (GRCm39)	D292E	unknown	Het
Skint4	T	A	4: 111,944,232 (GRCm39)	C23S	probably benign	Het
Slc22a28	A	C	19: 8,049,279 (GRCm39)	S323R	probably damaging	Het
Slc41a3	A	G	6: 90,617,891 (GRCm39)	T306A	probably benign	Het
Spata13	A	G	14: 60,987,445 (GRCm39)	M868V	probably damaging	Het
Spata6	T	G	4: 111,603,378 (GRCm39)	I31S	possibly damaging	Het
Tlk2	T	A	11: 105,172,046 (GRCm39)	S739T	unknown	Het
Trim10	T	C	17: 37,188,020 (GRCm39)	V412A	probably damaging	Het
Ttc3	T	A	16: 94,211,765 (GRCm39)	F377I	probably benign	Het
Uck1	T	A	2: 32,146,046 (GRCm39)	H283L	probably damaging	Het
Unc5a	T	C	13: 55,143,681 (GRCm39)	Y122H	possibly damaging	Het
Uncx	C	T	5: 139,530,377 (GRCm39)	R152*	probably null	Het
Usp44	A	G	10: 93,681,517 (GRCm39)		probably benign	Het
Vamp2	A	C	11: 68,980,564 (GRCm39)	D44A	probably benign	Het
Vmn2r83	A	G	10: 79,304,849 (GRCm39)	T20A	probably benign	Het
Vmn2r84	A	T	10: 130,221,784 (GRCm39)	I812N	probably damaging	Het
Vrtn	T	G	12: 84,695,943 (GRCm39)	L231R	probably damaging	Het
Wdr75	A	G	1: 45,859,333 (GRCm39)	T677A	probably damaging	Het
Xylt1	C	A	7: 117,148,100 (GRCm39)	S221R	possibly damaging	Het
Zscan22	A	G	7: 12,637,983 (GRCm39)	E125G	possibly damaging	Het
Zxdc	A	T	6: 90,350,698 (GRCm39)	H383L	probably damaging	Het

Other mutations in Sycp3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02103:Sycp3	APN	10	88,302,334 (GRCm39)	missense	possibly damaging	0.65
IGL02402:Sycp3	APN	10	88,302,425 (GRCm39)	intron	probably benign
R1468:Sycp3	UTSW	10	88,305,454 (GRCm39)	missense	possibly damaging	0.75
R1468:Sycp3	UTSW	10	88,305,454 (GRCm39)	missense	possibly damaging	0.75
R2857:Sycp3	UTSW	10	88,303,234 (GRCm39)	missense	probably damaging	1.00
R2858:Sycp3	UTSW	10	88,303,234 (GRCm39)	missense	probably damaging	1.00
R2897:Sycp3	UTSW	10	88,308,544 (GRCm39)	missense	possibly damaging	0.92
R2898:Sycp3	UTSW	10	88,308,544 (GRCm39)	missense	possibly damaging	0.92
R4194:Sycp3	UTSW	10	88,299,237 (GRCm39)	missense	probably benign	0.01
R5683:Sycp3	UTSW	10	88,308,797 (GRCm39)	missense	probably damaging	1.00
R6882:Sycp3	UTSW	10	88,308,791 (GRCm39)	nonsense	probably null
R7273:Sycp3	UTSW	10	88,305,428 (GRCm39)	missense	probably damaging	1.00
R7853:Sycp3	UTSW	10	88,302,368 (GRCm39)	missense	probably damaging	1.00
R8055:Sycp3	UTSW	10	88,298,438 (GRCm39)	missense	probably damaging	1.00
R8147:Sycp3	UTSW	10	88,298,467 (GRCm39)	critical splice donor site	probably null
R8720:Sycp3	UTSW	10	88,298,394 (GRCm39)	missense	probably benign	0.38
R8872:Sycp3	UTSW	10	88,302,388 (GRCm39)	missense	probably damaging	1.00
R9163:Sycp3	UTSW	10	88,299,734 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- GCTGAACTCCTTGGTTCCTAAA -3'
(R):5'- TCTCCACTGACTTCTAAGAAACATC -3'

Sequencing Primer
(F):5'- CCTTGATATTACTGAACAAACCTA -3'
(R):5'- ACATCAATTCTATGAAGGCATGAG -3'

Posted On

2019-06-07