Mutagenetix > Incidental Mutation

Incidental Mutation 'R5036:Sycp1'

389529

Institutional Source

Beutler Lab

Gene Symbol

Sycp1

Ensembl Gene

ENSMUSG00000027855

Gene Name

synaptonemal complex protein 1

Synonyms

SCP1

MMRRC Submission

042627-MU

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.477) question?

Stock #

R5036 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

102818499-102936100 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 102820600 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Methionine at position 899 (K899M)

Ref Sequence

ENSEMBL: ENSMUSP00000143651 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029448] [ENSMUST00000196988]

AlphaFold

Q62209

Predicted Effect

probably damaging
Transcript: ENSMUST00000029448
AA Change: K899M

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: K899M

Domain	Start	End	E-Value	Type
Pfam:SCP-1	28	809	N/A	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000196988
AA Change: K899M

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: K899M

Domain	Start	End	E-Value	Type
Pfam:SCP-1	28	809	N/A	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000198651

Meta Mutation Damage Score

0.0915

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 95.7%
20x: 90.1%

Validation Efficiency

100% (44/44)

MGI Phenotype

PHENOTYPE: Homozygous null mice display male and female infertility, azoospermia, small ovary, small testis and seminiferous tubules, absent ovarian follicles, and failure of synapse formation during meiosis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 35 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610021A01Rik	G	A	7: 41,626,154	G427D	possibly damaging	Het
Agbl5	G	A	5: 30,903,059	R141Q	probably damaging	Het
C4b	T	A	17: 34,740,445		probably null	Het
Cabyr	A	T	18: 12,751,246	E263D	probably damaging	Het
Car1	A	T	3: 14,776,239	D45E	possibly damaging	Het
Col25a1	T	C	3: 130,583,329		probably null	Het
Dnah6	G	T	6: 73,044,691	S3549R	probably benign	Het
Dync1h1	A	T	12: 110,630,535	I1639F	probably damaging	Het
Fhad1	A	T	4: 141,920,741	D271E	probably benign	Het
Gle1	T	C	2: 29,936,211	S101P	probably benign	Het
Gm4781	C	A	10: 100,396,989		noncoding transcript	Het
Gpatch3	A	G	4: 133,578,150	Y232C	probably damaging	Het
Gtf2ird2	A	G	5: 134,217,507	N869S	probably damaging	Het
Ifi204	G	A	1: 173,752,745	P400S	possibly damaging	Het
Ighv2-2	T	C	12: 113,588,472	T49A	possibly damaging	Het
Itsn1	T	A	16: 91,782,235		probably benign	Het
Mib2	A	T	4: 155,656,288	N626K	probably damaging	Het
Nf1	C	A	11: 79,446,864	Q1098K	probably damaging	Het
Odc1	C	A	12: 17,548,019	Q116K	probably damaging	Het
Otof	C	T	5: 30,384,439	E761K	possibly damaging	Het
Palld	A	T	8: 61,550,162	V301D	probably damaging	Het
Pask	A	T	1: 93,322,079	L533*	probably null	Het
Plekhh2	T	C	17: 84,571,761	S638P	probably damaging	Het
Scaf8	T	A	17: 3,164,262		probably benign	Het
Sdccag8	G	T	1: 177,011,975	R695L	probably damaging	Het
Serpina1c	A	G	12: 103,898,826	I187T	probably damaging	Het
Slitrk5	G	T	14: 111,680,884	G647W	possibly damaging	Het
Taok1	G	A	11: 77,549,331	R617C	probably benign	Het
Tbc1d32	A	C	10: 56,195,404	Y341*	probably null	Het
Tenm4	A	G	7: 96,694,790	N267D	probably damaging	Het
Tenm4	T	C	7: 96,852,561	V1287A	probably damaging	Het
Tsga10	A	T	1: 37,783,968	V488E	possibly damaging	Het
Ttc39c	G	T	18: 12,687,081		probably null	Het
Uck1	A	T	2: 32,258,466		probably benign	Het
Vmn2r98	A	G	17: 19,066,157	I306V	probably benign	Het

Other mutations in Sycp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00513:Sycp1	APN	3	102840962	missense	probably benign
IGL00833:Sycp1	APN	3	102876301	critical splice donor site	probably null
IGL01066:Sycp1	APN	3	102920634	missense	probably damaging	1.00
IGL01484:Sycp1	APN	3	102915867	missense	probably benign	0.01
IGL02139:Sycp1	APN	3	102865114	missense	probably benign	0.00
IGL02270:Sycp1	APN	3	102895943	missense	probably benign	0.12
IGL02347:Sycp1	APN	3	102893547	missense	probably benign	0.00
IGL02630:Sycp1	APN	3	102878764	splice site	probably benign
IGL02668:Sycp1	APN	3	102820531	splice site	probably benign
IGL02928:Sycp1	APN	3	102818818	utr 3 prime	probably benign
PIT4458001:Sycp1	UTSW	3	102934833	missense	probably benign	0.01
R0027:Sycp1	UTSW	3	102895910	missense	probably benign
R0282:Sycp1	UTSW	3	102915795	splice site	probably benign
R0462:Sycp1	UTSW	3	102819106	missense	possibly damaging	0.75
R0609:Sycp1	UTSW	3	102898849	splice site	probably null
R0837:Sycp1	UTSW	3	102915245	missense	probably benign	0.17
R1301:Sycp1	UTSW	3	102920622	missense	probably benign	0.02
R2408:Sycp1	UTSW	3	102925259	missense	probably damaging	1.00
R2449:Sycp1	UTSW	3	102925206	missense	probably benign	0.15
R2516:Sycp1	UTSW	3	102845066	missense	probably benign	0.09
R2880:Sycp1	UTSW	3	102818898	missense	probably damaging	0.99
R3410:Sycp1	UTSW	3	102841041	missense	possibly damaging	0.94
R3427:Sycp1	UTSW	3	102876350	missense	probably benign	0.00
R4538:Sycp1	UTSW	3	102840962	missense	probably benign
R4679:Sycp1	UTSW	3	102922462	critical splice acceptor site	probably null
R4707:Sycp1	UTSW	3	102853489	missense	possibly damaging	0.92
R4785:Sycp1	UTSW	3	102853489	missense	possibly damaging	0.92
R5017:Sycp1	UTSW	3	102895987	splice site	probably null
R5044:Sycp1	UTSW	3	102845054	missense	probably benign	0.03
R5070:Sycp1	UTSW	3	102920565	missense	probably damaging	0.97
R5079:Sycp1	UTSW	3	102878800	missense	possibly damaging	0.67
R5289:Sycp1	UTSW	3	102934253	missense	possibly damaging	0.85
R5393:Sycp1	UTSW	3	102841047	splice site	probably null
R5477:Sycp1	UTSW	3	102818890	missense	probably damaging	1.00
R5576:Sycp1	UTSW	3	102818902	missense	probably damaging	0.98
R5814:Sycp1	UTSW	3	102895897	missense	probably benign	0.03
R6291:Sycp1	UTSW	3	102908961	missense	probably damaging	1.00
R6460:Sycp1	UTSW	3	102925253	missense	probably damaging	1.00
R6527:Sycp1	UTSW	3	102898887	missense	probably benign	0.09
R6870:Sycp1	UTSW	3	102935603	missense	probably damaging	1.00
R6873:Sycp1	UTSW	3	102840980	missense	probably benign
R7037:Sycp1	UTSW	3	102898934	missense	possibly damaging	0.62
R7210:Sycp1	UTSW	3	102853492	missense	probably damaging	1.00
R7405:Sycp1	UTSW	3	102925227	missense	possibly damaging	0.72
R7604:Sycp1	UTSW	3	102913433	missense	probably damaging	0.98
R7733:Sycp1	UTSW	3	102895962	missense	probably benign	0.00
R7858:Sycp1	UTSW	3	102898957	missense	probably benign	0.09
R7909:Sycp1	UTSW	3	102820626	nonsense	probably null
R8109:Sycp1	UTSW	3	102851602	missense	probably benign	0.21
R8141:Sycp1	UTSW	3	102935569	missense	possibly damaging	0.73
R8289:Sycp1	UTSW	3	102841037	missense	probably benign	0.01
R8359:Sycp1	UTSW	3	102820593	missense	probably damaging	0.98
R8844:Sycp1	UTSW	3	102865105	missense	probably damaging	1.00
R9020:Sycp1	UTSW	3	102876337	missense	probably benign	0.01
R9149:Sycp1	UTSW	3	102851628	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGAATGTTACCGTTTGTCAGTACTG -3'
(R):5'- CCAGTTTCAAATTGCCTTCAAGTG -3'

Sequencing Primer
(F):5'- GACCCTTAATAACATATTTGGCTGTG -3'
(R):5'- GCCTTCAAGTGCATGAACTAG -3'

Posted On

2016-06-06