Mutagenetix > Incidental Mutation

Incidental Mutation 'R6500:Cyth3'

519666

Institutional Source

Beutler Lab

Gene Symbol

Cyth3

Ensembl Gene

ENSMUSG00000018001

Gene Name

cytohesin 3

Synonyms

Pscd3, Grp1, cytohesin 3

MMRRC Submission

044632-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.151) question?

Stock #

R6500 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

143608202-143696005 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 143693595 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 379 (I379F)

Ref Sequence

ENSEMBL: ENSMUSP00000112157 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000053287] [ENSMUST00000110727] [ENSMUST00000116456]

AlphaFold

O08967

PDB Structure

GRP1 PH DOMAIN WITH INS(1,3,4,5)P4 [X-RAY DIFFRACTION]
GRP1 PH DOMAIN (UNLIGANDED) [X-RAY DIFFRACTION]
Structure of the pleckstrin homology domain from GRP1 in complex with inositol(1,3,4,5,6)pentakisphosphate [X-RAY DIFFRACTION]
Structure of the pleckstrin homology domain from GRP1 in complex with inositol 1,3,4,5-tetrakisphosphate [X-RAY DIFFRACTION]
Triglycine variant of the Grp1 Pleckstrin Homology Domain unliganded [X-RAY DIFFRACTION]
Crystal Structure of Autoinhibited Form of Grp1 Arf GTPase Exchange Factor [X-RAY DIFFRACTION]
Crystal Structure of Autoinhibited Form of Grp1 Arf GTPase Exchange Factor [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000053287

SMART Domains

Protein: ENSMUSP00000053955
Gene: ENSMUSG00000051306

Domain	Start	End	E-Value	Type
low complexity region	65	77	N/A	INTRINSIC
Pfam:UCH	109	408	1.4e-46	PFAM
Pfam:UCH_1	110	391	1.4e-18	PFAM
low complexity region	470	490	N/A	INTRINSIC
low complexity region	567	579	N/A	INTRINSIC
low complexity region	604	613	N/A	INTRINSIC
low complexity region	634	645	N/A	INTRINSIC
low complexity region	954	962	N/A	INTRINSIC
low complexity region	1016	1031	N/A	INTRINSIC
low complexity region	1201	1219	N/A	INTRINSIC
low complexity region	1239	1255	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000110727
AA Change: I331F

PolyPhen 2 Score 0.908 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000106355
Gene: ENSMUSG00000018001
AA Change: I331F

Domain	Start	End	E-Value	Type
Sec7	15	200	1.5e-106	SMART
PH	217	334	1.1e-26	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000116456
AA Change: I379F

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000112157
Gene: ENSMUSG00000018001
AA Change: I379F

Domain	Start	End	E-Value	Type
low complexity region	3	10	N/A	INTRINSIC
low complexity region	14	35	N/A	INTRINSIC
Sec7	63	248	3.21e-104	SMART
PH	265	382	2.36e-24	SMART

Meta Mutation Damage Score

0.3897

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 95.0%

Validation Efficiency

98% (53/54)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the PSCD (pleckstrin homology, Sec7 and coiled-coil domains) family. PSCD family members have identical structural organization that consists of an N-terminal coiled-coil motif, a central Sec7 domain, and a C-terminal pleckstrin homology (PH) domain. The coiled-coil motif is involved in homodimerization, the Sec7 domain contains guanine-nucleotide exchange protein (GEP) activity, and the PH domain interacts with phospholipids and is responsible for association of PSCDs with membranes. Members of this family appear to mediate the regulation of protein sorting and membrane trafficking. This encoded protein is involved in the control of Golgi structure and function, and it may have a physiological role in regulating ADP-ribosylation factor protein 6 (ARF) functions, in addition to acting on ARF1. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam21	A	G	12: 81,606,380 (GRCm39)	F461L	probably benign	Het
Adamtsl3	C	A	7: 82,227,818 (GRCm39)	H1334Q	probably benign	Het
Adgrf1	A	G	17: 43,621,263 (GRCm39)	N500S	probably damaging	Het
Afdn	A	G	17: 14,042,634 (GRCm39)	D335G	possibly damaging	Het
Arhgap19	G	A	19: 41,775,077 (GRCm39)	T178M	probably damaging	Het
Chac2	T	C	11: 30,927,625 (GRCm39)	D86G	probably damaging	Het
Clhc1	T	C	11: 29,510,542 (GRCm39)	S209P	possibly damaging	Het
Col1a2	G	A	6: 4,515,517 (GRCm39)	G127S	unknown	Het
Coro2b	A	G	9: 62,396,606 (GRCm39)	F51L	probably benign	Het
Cux2	A	G	5: 122,002,789 (GRCm39)	S1139P	probably benign	Het
Dock2	A	T	11: 34,312,822 (GRCm39)	L240H	possibly damaging	Het
Ercc6	A	G	14: 32,248,780 (GRCm39)	K444E	probably damaging	Het
Fam3b	A	G	16: 97,302,101 (GRCm39)	L52P	possibly damaging	Het
Fat4	T	G	3: 39,035,418 (GRCm39)	Y3023*	probably null	Het
Gad1	A	T	2: 70,423,780 (GRCm39)	N396Y	probably damaging	Het
Gbp2b	A	G	3: 142,317,252 (GRCm39)	E536G	probably benign	Het
Gm11564	G	A	11: 99,706,061 (GRCm39)	T123I	unknown	Het
Herc2	G	T	7: 55,796,393 (GRCm39)	E1922*	probably null	Het
Hrh4	G	T	18: 13,155,525 (GRCm39)	V355F	probably damaging	Het
Isyna1	A	G	8: 71,047,339 (GRCm39)	I21V	probably damaging	Het
Jak1	T	C	4: 101,039,130 (GRCm39)	D165G	probably benign	Het
Klhl38	C	A	15: 58,185,809 (GRCm39)	G307*	probably null	Het
Krt77	T	C	15: 101,772,772 (GRCm39)	N269S	probably damaging	Het
Lrp4	T	A	2: 91,322,765 (GRCm39)	I1118N	possibly damaging	Het
Ly6i	T	C	15: 74,853,833 (GRCm39)	Y30C	probably damaging	Het
Magi2	A	G	5: 20,807,345 (GRCm39)	E620G	possibly damaging	Het
Mbl2	A	G	19: 30,216,839 (GRCm39)	D217G	possibly damaging	Het
Mogat2	T	A	7: 98,871,553 (GRCm39)	I253F	probably benign	Het
Mpped2	T	C	2: 106,691,925 (GRCm39)	L210P	probably damaging	Het
Nav3	C	A	10: 109,600,617 (GRCm39)	A1337S	probably damaging	Het
Ncaph2	T	A	15: 89,248,407 (GRCm39)	V206E	probably benign	Het
Nlgn1	T	C	3: 25,488,094 (GRCm39)	E747G	possibly damaging	Het
Nlrc3	C	T	16: 3,770,308 (GRCm39)	G237D	possibly damaging	Het
Nsun7	A	G	5: 66,452,827 (GRCm39)	D514G	probably benign	Het
Or10al5	C	G	17: 38,063,577 (GRCm39)	D277E	probably damaging	Het
Pals2	A	G	6: 50,175,146 (GRCm39)	K500E	possibly damaging	Het
Pcnx2	C	A	8: 126,480,224 (GRCm39)	V2028F	probably damaging	Het
Pdx1	G	T	5: 147,207,440 (GRCm39)	W131L	probably damaging	Het
Pkdrej	C	T	15: 85,703,747 (GRCm39)	V730I	probably damaging	Het
Plcg1	T	A	2: 160,596,487 (GRCm39)	Y669N	probably damaging	Het
Plpp1	G	T	13: 113,003,454 (GRCm39)	W226L	probably damaging	Het
Sfxn1	G	A	13: 54,242,918 (GRCm39)	V59I	probably benign	Het
Shank1	T	C	7: 43,976,645 (GRCm39)	I581T	unknown	Het
Slc35f6	A	C	5: 30,814,164 (GRCm39)	K150N	possibly damaging	Het
Slc5a7	A	T	17: 54,591,231 (GRCm39)	S234T	probably benign	Het
Smg6	C	T	11: 74,821,331 (GRCm39)	T534I	possibly damaging	Het
Ush2a	C	T	1: 188,573,724 (GRCm39)	T3649I	probably benign	Het
Vmn1r158	T	C	7: 22,490,078 (GRCm39)	T44A	possibly damaging	Het
Vmn1r217	A	T	13: 23,298,073 (GRCm39)	Y276*	probably null	Het
Vmn2r100	T	A	17: 19,742,355 (GRCm39)	I243N	probably damaging	Het
Vwde	T	C	6: 13,208,404 (GRCm39)		probably null	Het
Washc4	C	A	10: 83,394,687 (GRCm39)	P306T	probably damaging	Het
Wdhd1	C	T	14: 47,488,217 (GRCm39)		probably null	Het
Xpo6	T	C	7: 125,770,262 (GRCm39)		probably benign	Het

Other mutations in Cyth3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00953:Cyth3	APN	5	143,692,920 (GRCm39)	splice site	probably null
IGL01340:Cyth3	APN	5	143,670,190 (GRCm39)	nonsense	probably null
IGL01372:Cyth3	APN	5	143,678,393 (GRCm39)	missense	possibly damaging	0.93
IGL02092:Cyth3	APN	5	143,693,140 (GRCm39)	splice site	probably benign
IGL02850:Cyth3	APN	5	143,672,259 (GRCm39)	missense	probably damaging	0.97
IGL02892:Cyth3	APN	5	143,693,192 (GRCm39)	missense	possibly damaging	0.86
R0373:Cyth3	UTSW	5	143,670,181 (GRCm39)	utr 5 prime	probably benign
R0726:Cyth3	UTSW	5	143,678,397 (GRCm39)	missense	probably benign	0.00
R1217:Cyth3	UTSW	5	143,688,575 (GRCm39)	missense	probably damaging	1.00
R1552:Cyth3	UTSW	5	143,683,505 (GRCm39)	missense	probably benign	0.12
R1623:Cyth3	UTSW	5	143,687,127 (GRCm39)	missense	probably damaging	1.00
R1873:Cyth3	UTSW	5	143,683,516 (GRCm39)	missense	possibly damaging	0.54
R3788:Cyth3	UTSW	5	143,622,298 (GRCm39)	intron	probably benign
R4736:Cyth3	UTSW	5	143,670,234 (GRCm39)	critical splice donor site	probably null
R6824:Cyth3	UTSW	5	143,672,265 (GRCm39)	missense	probably damaging	1.00
R7105:Cyth3	UTSW	5	143,693,027 (GRCm39)	missense	probably benign	0.07
R7143:Cyth3	UTSW	5	143,670,151 (GRCm39)	missense	unknown
R7767:Cyth3	UTSW	5	143,693,229 (GRCm39)	missense	probably damaging	1.00
R7839:Cyth3	UTSW	5	143,683,509 (GRCm39)	missense	probably benign	0.01
R8220:Cyth3	UTSW	5	143,687,344 (GRCm39)	splice site	probably null
R8497:Cyth3	UTSW	5	143,678,328 (GRCm39)	missense	probably benign	0.02

Predicted Primers

PCR Primer
(F):5'- GGACACGTGTTTGCATGTC -3'
(R):5'- TGACCAATGTCCCAGAGCAC -3'

Sequencing Primer
(F):5'- CACGTGTTTGCATGTCAGGGG -3'
(R):5'- AGTGTATCTGCTGGAGTCT -3'

Posted On

2018-06-06