Mutagenetix > Incidental Mutation

Incidental Mutation 'R9104:Syde1'

691904

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

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9104 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

78420337-78427798 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 78421670 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Arginine at position 627 (H627R)

Ref Sequence

ENSEMBL: ENSMUSP00000043085 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040580] [ENSMUST00000105384] [ENSMUST00000218215] [ENSMUST00000218271] [ENSMUST00000218875] [ENSMUST00000218885] [ENSMUST00000220430]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000040580
AA Change: H627R

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000043085
Gene: ENSMUSG00000032714
AA Change: H627R

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: ENSMUST00000218271

Predicted Effect

probably benign
Transcript: ENSMUST00000218875

Predicted Effect

probably benign
Transcript: ENSMUST00000218885

Predicted Effect

probably benign
Transcript: ENSMUST00000219588

Predicted Effect

probably benign
Transcript: ENSMUST00000220430

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (69/69)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam26a	A	T	8: 44,023,108 (GRCm39)	N127K	probably damaging	Het
Adgrl3	C	T	5: 81,457,912 (GRCm39)	A14V	probably benign	Het
Adra2b	A	G	2: 127,205,858 (GRCm39)	Y125C	probably damaging	Het
Ahnak	T	A	19: 8,987,711 (GRCm39)	H2998Q	probably benign	Het
B3galt1	C	A	2: 67,948,406 (GRCm39)	H40Q	probably benign	Het
Best3	T	G	10: 116,860,680 (GRCm39)	L647V	probably benign	Het
Brip1	T	A	11: 86,077,897 (GRCm39)	E177V	possibly damaging	Het
C1qtnf6	T	C	15: 78,409,109 (GRCm39)	D246G	probably benign	Het
C4b	G	A	17: 34,948,233 (GRCm39)	T1622M	probably benign	Het
Catip	G	A	1: 74,401,682 (GRCm39)		probably null	Het
Ccdc138	T	C	10: 58,348,982 (GRCm39)	V176A	probably benign	Het
Ccdc85a	T	C	11: 28,526,879 (GRCm39)	H243R	probably damaging	Het
Cep19	C	T	16: 31,925,883 (GRCm39)	T97M	probably damaging	Het
Copz2	G	A	11: 96,747,514 (GRCm39)	D166N	possibly damaging	Het
Dedd	C	T	1: 171,168,572 (GRCm39)	L253F	probably damaging	Het
Dennd5a	A	G	7: 109,497,713 (GRCm39)		probably null	Het
Dpp10	A	T	1: 123,339,484 (GRCm39)	S348T	probably damaging	Het
Eci3	A	G	13: 35,144,382 (GRCm39)		probably null	Het
Egr4	A	G	6: 85,490,337 (GRCm39)	S15P	probably benign	Het
Elp6	A	G	9: 110,134,397 (GRCm39)	T12A	probably benign	Het
Ewsr1	G	T	11: 5,041,367 (GRCm39)	P113T	unknown	Het
Exosc10	T	G	4: 148,664,859 (GRCm39)	L789R	probably benign	Het
Flt4	A	G	11: 49,525,161 (GRCm39)	Y669C	probably damaging	Het
Foxred2	A	T	15: 77,836,517 (GRCm39)	F333I	probably damaging	Het
Frs2	G	T	10: 116,910,070 (GRCm39)	H431N	probably benign	Het
Gm10800	AAGAAAACTGAAAATCAT	A	2: 98,497,379 (GRCm39)		probably benign	Het
Gm19410	T	C	8: 36,247,621 (GRCm39)	Y478H	probably damaging	Het
Gm3629	G	A	14: 17,834,542 (GRCm39)	R150C		Het
Grik4	A	C	9: 42,571,168 (GRCm39)	L179R	probably damaging	Het
Gsdmc3	C	T	15: 63,730,941 (GRCm39)		probably null	Het
Il20ra	T	A	10: 19,635,364 (GRCm39)	M535K	probably benign	Het
Il9	A	G	13: 56,628,401 (GRCm39)	V96A	possibly damaging	Het
Itgal	A	G	7: 126,910,794 (GRCm39)	D592G	probably damaging	Het
Klk1b11	C	T	7: 43,427,875 (GRCm39)		probably benign	Het
Klk1b27	G	A	7: 43,705,310 (GRCm39)	W159*	probably null	Het
Mapk9	T	C	11: 49,760,000 (GRCm39)	Y105H	probably damaging	Het
Mmp7	A	G	9: 7,697,947 (GRCm39)		probably benign	Het
Muc2	T	C	7: 141,286,224 (GRCm39)	I118T	probably damaging	Het
N4bp2l2	T	C	5: 150,566,724 (GRCm39)	N131D	unknown	Het
Nbea	A	C	3: 55,862,809 (GRCm39)	S1814R	probably benign	Het
Nlrp9c	G	T	7: 26,081,837 (GRCm39)	L630I	probably benign	Het
Or1j8	T	C	2: 36,191,956 (GRCm39)	V135A		Het
Or6c76	T	C	10: 129,612,521 (GRCm39)	V261A	probably damaging	Het
Or8g27	G	A	9: 39,128,831 (GRCm39)	M59I	probably damaging	Het
Pbx3	C	A	2: 34,114,629 (GRCm39)	D102Y	probably damaging	Het
Pdia6	G	A	12: 17,320,492 (GRCm39)	V44I	probably benign	Het
Pkdcc	G	A	17: 83,528,471 (GRCm39)	R280H	probably damaging	Het
Ppm1h	A	G	10: 122,638,264 (GRCm39)	E178G	probably benign	Het
Prom1	C	T	5: 44,172,161 (GRCm39)	S619N	probably benign	Het
Prtg	A	C	9: 72,755,607 (GRCm39)	I270L	probably damaging	Het
Rfx6	A	T	10: 51,599,106 (GRCm39)	H487L	probably damaging	Het
Rpl18a	A	C	8: 71,348,788 (GRCm39)	Y63D	probably benign	Het
Rtl1	T	A	12: 109,560,718 (GRCm39)	M374L	probably benign	Het
Scaper	A	G	9: 55,819,400 (GRCm39)	L105P	unknown	Het
Slc16a13	T	A	11: 70,111,530 (GRCm39)		probably benign	Het
Slc6a13	A	G	6: 121,313,044 (GRCm39)	K487R	probably benign	Het
Slc7a11	T	A	3: 50,332,082 (GRCm39)	T459S	probably benign	Het
Smarcad1	A	G	6: 65,075,649 (GRCm39)	Q708R	probably benign	Het
Stat2	T	C	10: 128,117,111 (GRCm39)		probably null	Het
Tas2r113	G	A	6: 132,870,116 (GRCm39)	R48H	probably benign	Het
Tbc1d16	T	C	11: 119,038,626 (GRCm39)	Y690C	probably damaging	Het
Tchh	A	T	3: 93,354,610 (GRCm39)	H1350L	unknown	Het
Tex15	T	A	8: 34,060,950 (GRCm39)	Y127N	possibly damaging	Het
Thsd4	T	C	9: 59,964,179 (GRCm39)	T438A	possibly damaging	Het
Tubg1	A	G	11: 101,015,099 (GRCm39)	D216G	probably benign	Het
Tyk2	T	C	9: 21,026,762 (GRCm39)	D642G	possibly damaging	Het
Uqcc1	C	T	2: 155,743,217 (GRCm39)		probably null	Het
Uvssa	A	C	5: 33,571,404 (GRCm39)	K683Q	probably damaging	Het
Vmn1r59	A	T	7: 5,457,166 (GRCm39)	M198K	probably benign	Het
Zfp772	T	A	7: 7,207,190 (GRCm39)	H167L	possibly 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
R7239:Syde1	UTSW	10	78,424,615 (GRCm39)	missense	probably damaging	1.00
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
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'- ATCTTCGAAGTCGGTAGTGCC -3'
(R):5'- CCAATCATGGGTTGGAATCTAAGG -3'

Sequencing Primer
(F):5'- AAGTCGGTAGTGCCCCTCG -3'
(R):5'- TTGGAATCTAAGGAGGGTCATG -3'

Posted On

2021-12-30