Mutagenetix > Incidental Mutation

Incidental Mutation 'R2449:Sycp1'

248938

Institutional Source

Beutler Lab

Gene Symbol

Sycp1

Ensembl Gene

ENSMUSG00000027855

Gene Name

synaptonemal complex protein 1

Synonyms

SCP1

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.539) question?

Stock #

R2449 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

102725815-102843416 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 102832522 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 215 (I215V)

Ref Sequence

ENSEMBL: ENSMUSP00000143651 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029448] [ENSMUST00000196988] [ENSMUST00000199930]

AlphaFold

Q62209

Predicted Effect

probably benign
Transcript: ENSMUST00000029448
AA Change: I215V

PolyPhen 2 Score 0.152 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: I215V

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

Predicted Effect

probably benign
Transcript: ENSMUST00000196988
AA Change: I215V

PolyPhen 2 Score 0.152 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: I215V

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

Predicted Effect

probably benign
Transcript: ENSMUST00000199930
AA Change: I160V

PolyPhen 2 Score 0.061 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000143493
Gene: ENSMUSG00000027855
AA Change: I160V

Domain	Start	End	E-Value	Type
Pfam:SCP-1	28	95	2e-33	PFAM
Pfam:SCP-1	93	182	9.8e-53	PFAM

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.9%
20x: 94.0%

Validation Efficiency

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: 16 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	G	T	12: 71,211,320 (GRCm39)	E685*	probably null	Het
2700049A03Rik	A	T	12: 71,211,321 (GRCm39)	E685V	possibly damaging	Het
Cd83	A	T	13: 43,951,132 (GRCm39)	T95S	probably damaging	Het
Cdc27	T	C	11: 104,396,464 (GRCm39)	D819G	probably benign	Het
Hey2	A	T	10: 30,716,442 (GRCm39)	I64K	possibly damaging	Het
Il10rb	A	G	16: 91,208,791 (GRCm39)	H67R	probably benign	Het
Itgav	T	A	2: 83,599,094 (GRCm39)		probably null	Het
Lhx1	G	A	11: 84,412,564 (GRCm39)	R119C	probably damaging	Het
Ltbp3	G	A	19: 5,804,050 (GRCm39)	R854Q	probably benign	Het
Obscn	T	C	11: 59,022,472 (GRCm39)	R758G	possibly damaging	Het
Or12j2	A	T	7: 139,916,345 (GRCm39)	Q190L	probably benign	Het
Siglec1	T	C	2: 130,920,645 (GRCm39)	T720A	probably benign	Het
Trim63	A	G	4: 134,050,418 (GRCm39)	E234G	probably damaging	Het
Vmn2r56	C	T	7: 12,428,082 (GRCm39)	S728N	possibly damaging	Het
Wdr64	A	T	1: 175,526,479 (GRCm39)	I43L	probably benign	Het
Wsb1	T	C	11: 79,131,178 (GRCm39)	K406R	probably benign	Het

Other mutations in Sycp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00513:Sycp1	APN	3	102,748,278 (GRCm39)	missense	probably benign
IGL00833:Sycp1	APN	3	102,783,617 (GRCm39)	critical splice donor site	probably null
IGL01066:Sycp1	APN	3	102,827,950 (GRCm39)	missense	probably damaging	1.00
IGL01484:Sycp1	APN	3	102,823,183 (GRCm39)	missense	probably benign	0.01
IGL02139:Sycp1	APN	3	102,772,430 (GRCm39)	missense	probably benign	0.00
IGL02270:Sycp1	APN	3	102,803,259 (GRCm39)	missense	probably benign	0.12
IGL02347:Sycp1	APN	3	102,800,863 (GRCm39)	missense	probably benign	0.00
IGL02630:Sycp1	APN	3	102,786,080 (GRCm39)	splice site	probably benign
IGL02668:Sycp1	APN	3	102,727,847 (GRCm39)	splice site	probably benign
IGL02928:Sycp1	APN	3	102,726,134 (GRCm39)	utr 3 prime	probably benign
PIT4458001:Sycp1	UTSW	3	102,842,149 (GRCm39)	missense	probably benign	0.01
R0027:Sycp1	UTSW	3	102,803,226 (GRCm39)	missense	probably benign
R0282:Sycp1	UTSW	3	102,823,111 (GRCm39)	splice site	probably benign
R0462:Sycp1	UTSW	3	102,726,422 (GRCm39)	missense	possibly damaging	0.75
R0609:Sycp1	UTSW	3	102,806,165 (GRCm39)	splice site	probably null
R0837:Sycp1	UTSW	3	102,822,561 (GRCm39)	missense	probably benign	0.17
R1301:Sycp1	UTSW	3	102,827,938 (GRCm39)	missense	probably benign	0.02
R2408:Sycp1	UTSW	3	102,832,575 (GRCm39)	missense	probably damaging	1.00
R2516:Sycp1	UTSW	3	102,752,382 (GRCm39)	missense	probably benign	0.09
R2880:Sycp1	UTSW	3	102,726,214 (GRCm39)	missense	probably damaging	0.99
R3410:Sycp1	UTSW	3	102,748,357 (GRCm39)	missense	possibly damaging	0.94
R3427:Sycp1	UTSW	3	102,783,666 (GRCm39)	missense	probably benign	0.00
R4538:Sycp1	UTSW	3	102,748,278 (GRCm39)	missense	probably benign
R4679:Sycp1	UTSW	3	102,829,778 (GRCm39)	critical splice acceptor site	probably null
R4707:Sycp1	UTSW	3	102,760,805 (GRCm39)	missense	possibly damaging	0.92
R4785:Sycp1	UTSW	3	102,760,805 (GRCm39)	missense	possibly damaging	0.92
R5017:Sycp1	UTSW	3	102,803,303 (GRCm39)	splice site	probably null
R5036:Sycp1	UTSW	3	102,727,916 (GRCm39)	missense	probably damaging	1.00
R5044:Sycp1	UTSW	3	102,752,370 (GRCm39)	missense	probably benign	0.03
R5070:Sycp1	UTSW	3	102,827,881 (GRCm39)	missense	probably damaging	0.97
R5079:Sycp1	UTSW	3	102,786,116 (GRCm39)	missense	possibly damaging	0.67
R5289:Sycp1	UTSW	3	102,841,569 (GRCm39)	missense	possibly damaging	0.85
R5393:Sycp1	UTSW	3	102,748,363 (GRCm39)	splice site	probably null
R5477:Sycp1	UTSW	3	102,726,206 (GRCm39)	missense	probably damaging	1.00
R5576:Sycp1	UTSW	3	102,726,218 (GRCm39)	missense	probably damaging	0.98
R5814:Sycp1	UTSW	3	102,803,213 (GRCm39)	missense	probably benign	0.03
R6291:Sycp1	UTSW	3	102,816,277 (GRCm39)	missense	probably damaging	1.00
R6460:Sycp1	UTSW	3	102,832,569 (GRCm39)	missense	probably damaging	1.00
R6527:Sycp1	UTSW	3	102,806,203 (GRCm39)	missense	probably benign	0.09
R6870:Sycp1	UTSW	3	102,842,919 (GRCm39)	missense	probably damaging	1.00
R6873:Sycp1	UTSW	3	102,748,296 (GRCm39)	missense	probably benign
R7037:Sycp1	UTSW	3	102,806,250 (GRCm39)	missense	possibly damaging	0.62
R7210:Sycp1	UTSW	3	102,760,808 (GRCm39)	missense	probably damaging	1.00
R7405:Sycp1	UTSW	3	102,832,543 (GRCm39)	missense	possibly damaging	0.72
R7604:Sycp1	UTSW	3	102,820,749 (GRCm39)	missense	probably damaging	0.98
R7733:Sycp1	UTSW	3	102,803,278 (GRCm39)	missense	probably benign	0.00
R7858:Sycp1	UTSW	3	102,806,273 (GRCm39)	missense	probably benign	0.09
R7909:Sycp1	UTSW	3	102,727,942 (GRCm39)	nonsense	probably null
R8109:Sycp1	UTSW	3	102,758,918 (GRCm39)	missense	probably benign	0.21
R8141:Sycp1	UTSW	3	102,842,885 (GRCm39)	missense	possibly damaging	0.73
R8289:Sycp1	UTSW	3	102,748,353 (GRCm39)	missense	probably benign	0.01
R8359:Sycp1	UTSW	3	102,727,909 (GRCm39)	missense	probably damaging	0.98
R8844:Sycp1	UTSW	3	102,772,421 (GRCm39)	missense	probably damaging	1.00
R9020:Sycp1	UTSW	3	102,783,653 (GRCm39)	missense	probably benign	0.01
R9149:Sycp1	UTSW	3	102,758,944 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGCCTGAAGACAATAAATCTAGAC -3'
(R):5'- CCCCAGGCCAGTGAGTTTAT -3'

Sequencing Primer
(F):5'- AAGATCATGTCTTATATTCCCCCTC -3'
(R):5'- GCAATGCCAGTTACAGTTCAG -3'

Posted On

2014-11-12