Mutagenetix > Incidental Mutation

Incidental Mutation 'R9110:Arfgap1'

692185

Institutional Source

Beutler Lab

Gene Symbol

Arfgap1

Ensembl Gene

ENSMUSG00000027575

Gene Name

ADP-ribosylation factor GTPase activating protein 1

Synonyms

ARF1 GAP

MMRRC Submission

068919-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.200) question?

Stock #

R9110 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

180609018-180624319 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 180615330 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 174 (S174T)

Ref Sequence

ENSEMBL: ENSMUSP00000104490 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029092] [ENSMUST00000108859] [ENSMUST00000108860] [ENSMUST00000108861] [ENSMUST00000108862] [ENSMUST00000184394] [ENSMUST00000185115]

AlphaFold

Q9EPJ9

Predicted Effect

possibly damaging
Transcript: ENSMUST00000029092
AA Change: S174T

PolyPhen 2 Score 0.812 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000029092
Gene: ENSMUSG00000027575
AA Change: S174T

Domain	Start	End	E-Value	Type
ArfGap	7	124	2.4e-54	SMART
low complexity region	149	160	N/A	INTRINSIC
PDB:2M0W\|A	198	220	1e-6	PDB
low complexity region	310	327	N/A	INTRINSIC
low complexity region	334	347	N/A	INTRINSIC
low complexity region	359	392	N/A	INTRINSIC
low complexity region	394	401	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108859
AA Change: S174T

PolyPhen 2 Score 0.125 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000104487
Gene: ENSMUSG00000027575
AA Change: S174T

Domain	Start	End	E-Value	Type
ArfGap	7	124	2.4e-54	SMART
low complexity region	149	160	N/A	INTRINSIC
PDB:2M0W\|A	198	220	1e-6	PDB
low complexity region	288	305	N/A	INTRINSIC
low complexity region	312	325	N/A	INTRINSIC
low complexity region	337	370	N/A	INTRINSIC
low complexity region	372	379	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108860
AA Change: S174T

PolyPhen 2 Score 0.125 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000104488
Gene: ENSMUSG00000027575
AA Change: S174T

Domain	Start	End	E-Value	Type
ArfGap	7	124	2.4e-54	SMART
low complexity region	149	160	N/A	INTRINSIC
PDB:2M0W\|A	198	220	1e-6	PDB
low complexity region	288	305	N/A	INTRINSIC
low complexity region	312	325	N/A	INTRINSIC
low complexity region	337	370	N/A	INTRINSIC
low complexity region	372	379	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000108861
AA Change: S174T

PolyPhen 2 Score 0.812 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000104489
Gene: ENSMUSG00000027575
AA Change: S174T

Domain	Start	End	E-Value	Type
ArfGap	7	124	2.4e-54	SMART
low complexity region	149	160	N/A	INTRINSIC
PDB:2M0W\|A	198	220	1e-6	PDB
low complexity region	290	307	N/A	INTRINSIC
low complexity region	314	327	N/A	INTRINSIC
low complexity region	339	372	N/A	INTRINSIC
low complexity region	374	381	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000108862
AA Change: S174T

PolyPhen 2 Score 0.812 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000104490
Gene: ENSMUSG00000027575
AA Change: S174T

Domain	Start	End	E-Value	Type
ArfGap	7	124	2.4e-54	SMART
low complexity region	149	160	N/A	INTRINSIC
PDB:2M0W\|A	198	220	1e-6	PDB
low complexity region	290	307	N/A	INTRINSIC
low complexity region	314	327	N/A	INTRINSIC
low complexity region	339	372	N/A	INTRINSIC
low complexity region	374	381	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000184394
AA Change: S174T

PolyPhen 2 Score 0.943 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000138843
Gene: ENSMUSG00000027575
AA Change: S174T

Domain	Start	End	E-Value	Type
ArfGap	7	124	2.4e-54	SMART
low complexity region	149	160	N/A	INTRINSIC
PDB:2M0W\|A	198	220	1e-6	PDB
low complexity region	298	315	N/A	INTRINSIC
low complexity region	322	335	N/A	INTRINSIC
low complexity region	347	380	N/A	INTRINSIC
low complexity region	382	389	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000185115
AA Change: S174T

PolyPhen 2 Score 0.164 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000139222
Gene: ENSMUSG00000027575
AA Change: S174T

Domain	Start	End	E-Value	Type
ArfGap	7	124	2.4e-54	SMART
low complexity region	149	160	N/A	INTRINSIC
PDB:2M0W\|A	198	220	1e-6	PDB
low complexity region	320	337	N/A	INTRINSIC
low complexity region	344	357	N/A	INTRINSIC
low complexity region	369	402	N/A	INTRINSIC
low complexity region	404	411	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

100% (61/61)

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 GTPase-activating protein, which associates with the Golgi apparatus and which interacts with ADP-ribosylation factor 1. The encoded protein promotes hydrolysis of ADP-ribosylation factor 1-bound GTP and is required for the dissociation of coat proteins from Golgi-derived membranes and vesicles. Dissociation of the coat proteins is required for the fusion of these vesicles with target compartments. The activity of this protein is stimulated by phosphoinosides and inhibited by phosphatidylcholine. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca14	A	G	7: 119,831,615 (GRCm39)		probably benign	Het
Adam20	A	G	8: 41,248,907 (GRCm39)	D339G	probably benign	Het
Adam3	T	A	8: 25,193,821 (GRCm39)	Y397F	probably benign	Het
Ago3	C	T	4: 126,248,829 (GRCm39)	G574E	probably damaging	Het
Angptl4	T	A	17: 33,999,800 (GRCm39)	Y133F	probably benign	Het
Ankrd61	T	C	5: 143,831,759 (GRCm39)	D15G	possibly damaging	Het
Arhgap12	T	C	18: 6,034,539 (GRCm39)	D549G	possibly damaging	Het
Arhgap25	T	C	6: 87,453,254 (GRCm39)	E182G	probably benign	Het
Astn1	T	G	1: 158,496,327 (GRCm39)	I1127S	probably benign	Het
Bivm	T	C	1: 44,168,526 (GRCm39)		probably null	Het
Cdc42bpa	T	A	1: 179,945,258 (GRCm39)	S952T	possibly damaging	Het
Cfap44	T	A	16: 44,255,923 (GRCm39)	L1005Q	probably damaging	Het
Cmklr1	G	C	5: 113,752,043 (GRCm39)	H319Q	probably benign	Het
Cog1	T	C	11: 113,544,807 (GRCm39)	F330L	possibly damaging	Het
Dnah2	T	G	11: 69,435,208 (GRCm39)	D54A	probably benign	Het
Dntt	A	T	19: 41,044,197 (GRCm39)		probably null	Het
Eml2	A	G	7: 18,925,620 (GRCm39)	S240G	probably benign	Het
Fam174b	G	A	7: 73,416,371 (GRCm39)		probably benign	Het
Fancd2	T	C	6: 113,512,762 (GRCm39)	S33P	possibly damaging	Het
Fars2	A	T	13: 36,430,402 (GRCm39)	M277L	probably benign	Het
Ifnar1	G	A	16: 91,302,150 (GRCm39)	G542S	probably benign	Het
Itih5	T	C	2: 10,191,831 (GRCm39)	V122A	probably benign	Het
Jph3	A	G	8: 122,516,201 (GRCm39)	I740V	probably benign	Het
Krtap16-1	C	T	11: 99,877,386 (GRCm39)	C6Y	probably benign	Het
Mettl25b	G	A	3: 87,834,978 (GRCm39)	H57Y	probably benign	Het
Mpeg1	A	T	19: 12,440,014 (GRCm39)	T491S	probably benign	Het
Mroh8	T	A	2: 157,055,605 (GRCm39)	I998L	possibly damaging	Het
Nrxn1	G	A	17: 90,869,233 (GRCm39)	Q124*	probably null	Het
Nup188	T	A	2: 30,222,461 (GRCm39)	S1028T	possibly damaging	Het
Nxf1	A	T	19: 8,745,118 (GRCm39)	H456L	probably damaging	Het
Or2aj6	T	A	16: 19,443,743 (GRCm39)	I36F	possibly damaging	Het
Or2n1d	C	A	17: 38,646,434 (GRCm39)	P129T	probably damaging	Het
Or5af2	T	A	11: 58,707,959 (GRCm39)	S42T	possibly damaging	Het
Or5w19	T	A	2: 87,698,543 (GRCm39)	D69E	probably damaging	Het
Or6c66	T	A	10: 129,461,820 (GRCm39)	I37F	possibly damaging	Het
Otx2	T	C	14: 48,896,227 (GRCm39)	N277S	probably damaging	Het
Pax4	T	C	6: 28,445,201 (GRCm39)	N158S	probably benign	Het
Pgm2	T	G	5: 64,261,159 (GRCm39)	S218A	probably benign	Het
Plb1	T	C	5: 32,521,402 (GRCm39)	S1418P	probably benign	Het
Prkd3	T	A	17: 79,292,751 (GRCm39)	D107V	probably damaging	Het
Prl2a1	A	G	13: 27,992,398 (GRCm39)	E174G	probably benign	Het
Prr7	C	T	13: 55,620,574 (GRCm39)	P194L	probably damaging	Het
Psmd2	T	C	16: 20,470,994 (GRCm39)	S46P	probably damaging	Het
Ptbp2	C	T	3: 119,541,258 (GRCm39)	A231T	possibly damaging	Het
Rae1	A	G	2: 172,854,016 (GRCm39)	T265A	probably benign	Het
Sct	T	C	7: 140,859,007 (GRCm39)	E2G	unknown	Het
Sec14l3	T	G	11: 4,015,007 (GRCm39)		probably null	Het
Sfxn3	T	A	19: 45,038,727 (GRCm39)	N131K	probably damaging	Het
Slc18a2	A	T	19: 59,282,326 (GRCm39)	D511V	probably benign	Het
Slc20a2	T	C	8: 23,025,457 (GRCm39)	I53T	probably damaging	Het
Smad4	T	C	18: 73,782,941 (GRCm39)	D331G	probably damaging	Het
Srms	C	T	2: 180,848,050 (GRCm39)	R485H		Het
Szt2	C	A	4: 118,242,630 (GRCm39)	A1486S	possibly damaging	Het
Tmem87b	C	T	2: 128,684,615 (GRCm39)	Q459*	probably null	Het
Vdr	A	T	15: 97,782,753 (GRCm39)	I23N	probably damaging	Het
Vmn1r204	T	C	13: 22,740,564 (GRCm39)	V65A	possibly damaging	Het
Vps33b	A	G	7: 79,939,743 (GRCm39)	D498G	probably benign	Het
Zfp442	T	A	2: 150,250,093 (GRCm39)	Y603F	probably benign	Het
Zfp853	T	A	5: 143,275,320 (GRCm39)	Q115L	unknown	Het
Zmiz2	C	A	11: 6,348,271 (GRCm39)	Q303K	probably benign	Het

Other mutations in Arfgap1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01518:Arfgap1	APN	2	180,614,518 (GRCm39)	missense	probably benign	0.01
IGL01521:Arfgap1	APN	2	180,613,371 (GRCm39)	missense	probably damaging	1.00
IGL02118:Arfgap1	APN	2	180,622,237 (GRCm39)	missense	possibly damaging	0.89
R1858:Arfgap1	UTSW	2	180,615,881 (GRCm39)	missense	probably damaging	1.00
R2060:Arfgap1	UTSW	2	180,614,575 (GRCm39)	missense	probably benign
R2509:Arfgap1	UTSW	2	180,615,846 (GRCm39)	splice site	probably benign
R4423:Arfgap1	UTSW	2	180,622,869 (GRCm39)	missense	probably benign	0.00
R4424:Arfgap1	UTSW	2	180,622,869 (GRCm39)	missense	probably benign	0.00
R4425:Arfgap1	UTSW	2	180,622,869 (GRCm39)	missense	probably benign	0.00
R4569:Arfgap1	UTSW	2	180,618,166 (GRCm39)	splice site	probably benign
R5668:Arfgap1	UTSW	2	180,615,912 (GRCm39)	missense	possibly damaging	0.81
R5834:Arfgap1	UTSW	2	180,622,955 (GRCm39)	missense	probably benign	0.01
R5915:Arfgap1	UTSW	2	180,620,215 (GRCm39)	missense	possibly damaging	0.88
R6819:Arfgap1	UTSW	2	180,613,478 (GRCm39)	critical splice donor site	probably null
R7011:Arfgap1	UTSW	2	180,613,935 (GRCm39)	missense	probably damaging	1.00
R7017:Arfgap1	UTSW	2	180,618,097 (GRCm39)	splice site	probably null
R7069:Arfgap1	UTSW	2	180,615,913 (GRCm39)	missense	probably benign	0.01
R7350:Arfgap1	UTSW	2	180,612,869 (GRCm39)	missense	possibly damaging	0.51
R8104:Arfgap1	UTSW	2	180,621,022 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- GGTACCTCTTTGACCCCAAC -3'
(R):5'- CACTCAAACCTAGGCCATCTTG -3'

Sequencing Primer
(F):5'- ACCTCTTTGACCCCAACTATGATATG -3'
(R):5'- GTGGACCCCAGATCACACATACTG -3'

Posted On

2021-12-30