Mutagenetix > Incidental Mutation

Incidental Mutation 'R7239:Syde1'

563089

Institutional Source

Beutler Lab

Gene Symbol

Syde1

Ensembl Gene

ENSMUSG00000032714

Gene Name

synapse defective 1, Rho GTPase, homolog 1 (C. elegans)

Synonyms

1200008N06Rik, mSYD1A

MMRRC Submission

045346-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7239 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

78420337-78427798 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 78424615 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 406 (R406C)

Ref Sequence

ENSEMBL: ENSMUSP00000043085 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040580] [ENSMUST00000105384] [ENSMUST00000218215] [ENSMUST00000218875] [ENSMUST00000218885]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000040580
AA Change: R406C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000043085
Gene: ENSMUSG00000032714
AA Change: R406C

Domain	Start	End	E-Value	Type
low complexity region	37	45	N/A	INTRINSIC
low complexity region	56	69	N/A	INTRINSIC
low complexity region	114	127	N/A	INTRINSIC
low complexity region	147	160	N/A	INTRINSIC
low complexity region	176	191	N/A	INTRINSIC
low complexity region	321	335	N/A	INTRINSIC
RhoGAP	411	601	1.49e-56	SMART
low complexity region	638	652	N/A	INTRINSIC
low complexity region	681	694	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000105384

SMART Domains

Protein: ENSMUSP00000101023
Gene: ENSMUSG00000032763

Domain	Start	End	E-Value	Type
transmembrane domain	12	34	N/A	INTRINSIC
Pfam:TPP_enzyme_N	52	220	1.4e-53	PFAM
Pfam:TPP_enzyme_M	273	405	2.1e-16	PFAM
Pfam:TPP_enzyme_C	467	618	3.1e-28	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000218215

Predicted Effect

probably benign
Transcript: ENSMUST00000218875

Predicted Effect

probably benign
Transcript: ENSMUST00000218885

Predicted Effect

probably benign
Transcript: ENSMUST00000219588

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

99% (76/77)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a Rho GTPase-activating protein highly expressed in placenta. The encoded protein is involved in cytoskeletal remodeling and trophoblast cell migration. Decreased expression of this gene has been associated with intrauterine growth restriction (IUGR). [provided by RefSeq, Feb 2017]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit reduced miniature excitatory postsynaptic current freuqency and docked vesciles in CA1 synpases. Mice homozygous for another allele exhibit reduced embryos and placental weight with abnormal placenta morphology and placental vasculature. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510009E07Rik	A	G	16: 21,472,268 (GRCm39)	V144A	probably damaging	Het
Abca5	A	T	11: 110,217,530 (GRCm39)	Y109N	possibly damaging	Het
Abcb5	T	C	12: 118,892,460 (GRCm39)	Q433R	probably benign	Het
Adamts7	G	A	9: 90,068,610 (GRCm39)		probably null	Het
Adgrv1	T	C	13: 81,624,731 (GRCm39)	D3746G	possibly damaging	Het
Arhgap29	C	T	3: 121,782,599 (GRCm39)	S159L	probably benign	Het
Arhgap5	T	A	12: 52,564,159 (GRCm39)	C377S	probably benign	Het
Atp1a3	G	A	7: 24,700,129 (GRCm39)	P77L	probably damaging	Het
B4galt1	T	C	4: 40,812,754 (GRCm39)	D257G	probably damaging	Het
Bin1	T	A	18: 32,539,224 (GRCm39)	N52K	probably damaging	Het
Catsperg2	A	G	7: 29,409,507 (GRCm39)	M562T	probably benign	Het
Ccdc33	G	A	9: 57,940,192 (GRCm39)	Q713*	probably null	Het
Cd96	A	T	16: 45,929,477 (GRCm39)	L156Q	probably damaging	Het
Clpb	A	G	7: 101,360,662 (GRCm39)	T231A	probably damaging	Het
Dnaaf9	C	A	2: 130,648,708 (GRCm39)	R258L	unknown	Het
Dnmt3a	A	T	12: 3,922,850 (GRCm39)	Q151L	probably benign	Het
Dock2	C	T	11: 34,181,677 (GRCm39)	V1629M	probably benign	Het
Edem1	G	A	6: 108,831,341 (GRCm39)	D601N	probably benign	Het
Eno2	C	T	6: 124,745,228 (GRCm39)	V20M	probably damaging	Het
Eny2	A	C	15: 44,297,250 (GRCm39)	D52A	probably benign	Het
Esp36	T	C	17: 38,728,132 (GRCm39)	R93G	possibly damaging	Het
Fam227a	A	G	15: 79,518,263 (GRCm39)		probably null	Het
Fat4	C	A	3: 39,037,989 (GRCm39)	H3880Q	possibly damaging	Het
Fbxw24	A	T	9: 109,434,598 (GRCm39)	V334E	possibly damaging	Het
Flrt1	T	C	19: 7,073,329 (GRCm39)	Q406R	probably benign	Het
Frmpd2	A	G	14: 33,274,034 (GRCm39)	N1092S	probably benign	Het
Gm904	C	A	13: 50,799,287 (GRCm39)	T82K	probably benign	Het
Gnas	G	C	2: 174,140,408 (GRCm39)	G252R	unknown	Het
Gpatch2l	A	G	12: 86,307,349 (GRCm39)		probably null	Het
H2ac6	A	T	13: 23,867,593 (GRCm39)	I103N	probably damaging	Het
Ift74	T	C	4: 94,541,187 (GRCm39)	V204A	probably benign	Het
Ikzf4	A	G	10: 128,477,113 (GRCm39)	L119P	probably damaging	Het
Ing3	G	A	6: 21,952,193 (GRCm39)	E56K	probably damaging	Het
Klhl25	T	C	7: 75,516,516 (GRCm39)	I474T	probably benign	Het
Klhl5	T	C	5: 65,318,529 (GRCm39)	V556A	probably damaging	Het
Krt14	A	T	11: 100,095,081 (GRCm39)	M382K	probably benign	Het
Lmcd1	T	C	6: 112,292,745 (GRCm39)	V199A	possibly damaging	Het
Lpcat4	T	A	2: 112,073,052 (GRCm39)	F200I	possibly damaging	Het
Lrp1b	T	C	2: 40,894,725 (GRCm39)	T2282A		Het
Lrrk1	T	C	7: 65,911,903 (GRCm39)	T1886A	probably benign	Het
Meis2	T	C	2: 115,889,484 (GRCm39)		probably null	Het
Mki67	C	T	7: 135,301,905 (GRCm39)	R1043K	possibly damaging	Het
Myct1	G	T	10: 5,554,601 (GRCm39)	R156L	possibly damaging	Het
Nckap5l	G	T	15: 99,324,090 (GRCm39)	H804Q	probably damaging	Het
Ndst3	T	G	3: 123,400,555 (GRCm39)	E450D	probably damaging	Het
Nipbl	A	T	15: 8,321,619 (GRCm39)		probably null	Het
Npy	A	G	6: 49,800,587 (GRCm39)	N4D	probably benign	Het
Or7g35	A	T	9: 19,496,487 (GRCm39)	Y218F	probably damaging	Het
Osgin2	T	C	4: 16,008,748 (GRCm39)	S18G	probably benign	Het
Pcdha9	T	G	18: 37,131,551 (GRCm39)	F207V	probably benign	Het
Pcdhb13	A	T	18: 37,577,697 (GRCm39)	I692F	probably damaging	Het
Pde3b	T	A	7: 114,015,384 (GRCm39)	V200E	probably damaging	Het
Ppp6r3	A	T	19: 3,543,981 (GRCm39)	L345I	probably benign	Het
Psd2	G	A	18: 36,113,472 (GRCm39)	A315T	probably damaging	Het
Rnf111	G	A	9: 70,376,655 (GRCm39)	T328I	probably damaging	Het
Rnf213	T	C	11: 119,349,614 (GRCm39)	L3825P		Het
Rtl1	C	T	12: 109,558,909 (GRCm39)	V977I	probably benign	Het
Scn1a	G	A	2: 66,108,000 (GRCm39)		probably null	Het
Slc25a2	G	T	18: 37,770,748 (GRCm39)	N260K	probably benign	Het
Sprtn	T	C	8: 125,626,983 (GRCm39)	V121A	probably damaging	Het
Ssx2ip	T	G	3: 146,133,771 (GRCm39)	L260W	probably damaging	Het
Tab1	A	G	15: 80,017,372 (GRCm39)	R6G	probably benign	Het
Tenm4	G	A	7: 96,202,703 (GRCm39)	R106H	probably benign	Het
Tenm4	G	A	7: 96,385,020 (GRCm39)	V526I	possibly damaging	Het
Tfap2b	T	C	1: 19,304,404 (GRCm39)	F405L	probably damaging	Het
Trbv13-1	C	A	6: 41,093,325 (GRCm39)	T87K	probably benign	Het
Trmt44	G	T	5: 35,732,130 (GRCm39)	A87E	probably benign	Het
Ttll3	CAAAGTAA	CAAAGTAAAGTAA	6: 113,376,118 (GRCm39)		probably null	Het
Ttn	T	C	2: 76,617,634 (GRCm39)	D16279G	probably damaging	Het
Ttn	G	A	2: 76,711,672 (GRCm39)	R8290C	unknown	Het
Ugt2b37	T	A	5: 87,402,590 (GRCm39)	I14L	probably benign	Het
Vmn1r13	A	T	6: 57,187,611 (GRCm39)	M257L	probably benign	Het
Vmn1r184	C	T	7: 25,966,602 (GRCm39)	P116L	possibly damaging	Het
Zfp426	T	C	9: 20,381,887 (GRCm39)	T367A	probably benign	Het
Zfp647	A	T	15: 76,795,956 (GRCm39)	C235S	probably damaging	Het

Other mutations in Syde1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00229:Syde1	APN	10	78,421,643 (GRCm39)	missense	probably damaging	1.00
IGL01285:Syde1	APN	10	78,424,721 (GRCm39)	missense	probably damaging	1.00
IGL01529:Syde1	APN	10	78,426,015 (GRCm39)	missense	probably benign
IGL01869:Syde1	APN	10	78,424,753 (GRCm39)	missense	possibly damaging	0.93
IGL02098:Syde1	APN	10	78,425,205 (GRCm39)	missense	probably damaging	1.00
IGL03187:Syde1	APN	10	78,424,943 (GRCm39)	missense	possibly damaging	0.79
R0014:Syde1	UTSW	10	78,425,868 (GRCm39)	missense	probably benign
R0561:Syde1	UTSW	10	78,425,210 (GRCm39)	missense	probably damaging	1.00
R0605:Syde1	UTSW	10	78,424,929 (GRCm39)	unclassified	probably benign
R1713:Syde1	UTSW	10	78,421,530 (GRCm39)	missense	probably damaging	1.00
R1756:Syde1	UTSW	10	78,422,814 (GRCm39)	missense	probably benign
R4491:Syde1	UTSW	10	78,426,062 (GRCm39)	missense	probably benign	0.00
R4846:Syde1	UTSW	10	78,424,731 (GRCm39)	missense	probably damaging	0.99
R5092:Syde1	UTSW	10	78,425,252 (GRCm39)	missense	probably benign
R5287:Syde1	UTSW	10	78,425,871 (GRCm39)	missense	probably benign
R5611:Syde1	UTSW	10	78,421,725 (GRCm39)	missense	probably benign
R5951:Syde1	UTSW	10	78,425,150 (GRCm39)	missense	possibly damaging	0.87
R5957:Syde1	UTSW	10	78,425,951 (GRCm39)	missense	probably damaging	1.00
R6169:Syde1	UTSW	10	78,421,938 (GRCm39)	missense	probably damaging	1.00
R7083:Syde1	UTSW	10	78,422,903 (GRCm39)	missense	probably benign	0.44
R7150:Syde1	UTSW	10	78,422,032 (GRCm39)	nonsense	probably null
R7799:Syde1	UTSW	10	78,425,741 (GRCm39)	missense	probably benign
R7947:Syde1	UTSW	10	78,425,916 (GRCm39)	missense	probably damaging	1.00
R8876:Syde1	UTSW	10	78,425,325 (GRCm39)	missense	probably damaging	1.00
R8946:Syde1	UTSW	10	78,424,683 (GRCm39)	missense	probably damaging	0.99
R9104:Syde1	UTSW	10	78,421,670 (GRCm39)	missense	probably benign	0.01
R9132:Syde1	UTSW	10	78,425,340 (GRCm39)	missense	probably benign
R9703:Syde1	UTSW	10	78,421,557 (GRCm39)	missense	probably damaging	1.00
R9728:Syde1	UTSW	10	78,424,638 (GRCm39)	frame shift	probably null
Z1176:Syde1	UTSW	10	78,421,965 (GRCm39)	missense	possibly damaging	0.94

Predicted Primers

PCR Primer
(F):5'- CTCCAAAGACTGAGCTCCATG -3'
(R):5'- AGGATAAAATTGCCTCAGTCCTCC -3'

Sequencing Primer
(F):5'- CTGAGCTCCATGAGGGCTAAG -3'
(R):5'- CCTTGCATCTTTAGGGTGCCAAG -3'

Posted On

2019-06-26