Mutagenetix > Incidental Mutation

Incidental Mutation 'R0165:Agap3'

24099

Institutional Source

Beutler Lab

Gene Symbol

Agap3

Ensembl Gene

ENSMUSG00000023353

Gene Name

ArfGAP with GTPase domain, ankyrin repeat and PH domain 3

Synonyms

Crag, Centg3, MRIP-1

MMRRC Submission

038441-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.126) question?

Stock #

R0165 (G1)

Quality Score

174

Status

Validated (trace)

Chromosome

Chromosomal Location

24452177-24502047 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 24479745 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 544 (T544A)

Ref Sequence

ENSEMBL: ENSMUSP00000142529 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000024123] [ENSMUST00000199856] [ENSMUST00000212381]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000024123
AA Change: T361A

PolyPhen 2 Score 0.555 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000024123
Gene: ENSMUSG00000023353
AA Change: T361A

Domain	Start	End	E-Value	Type
low complexity region	4	59	N/A	INTRINSIC
Pfam:Ras	128	286	1.2e-18	PFAM
low complexity region	328	345	N/A	INTRINSIC
PH	403	642	2.76e-16	SMART
ArfGap	661	781	9.17e-51	SMART
ANK	820	849	2.43e1	SMART
ANK	853	885	9.17e1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000197513

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199250

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199647

Predicted Effect

probably damaging
Transcript: ENSMUST00000199856
AA Change: T544A

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000142529
Gene: ENSMUSG00000023353
AA Change: T544A

Domain	Start	End	E-Value	Type
low complexity region	40	50	N/A	INTRINSIC
low complexity region	66	108	N/A	INTRINSIC
low complexity region	242	255	N/A	INTRINSIC
low complexity region	278	292	N/A	INTRINSIC
small_GTPase	307	473	3.2e-11	SMART
low complexity region	511	528	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000212381
AA Change: T361A

PolyPhen 2 Score 0.794 (Sensitivity: 0.85; Specificity: 0.93)

Meta Mutation Damage Score

0.0723

Coding Region Coverage

1x: 99.4%
3x: 98.5%
10x: 96.2%
20x: 91.4%

Validation Efficiency

96% (81/84)

Allele List at MGI

Other mutations in this stock

Total: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410089E03Rik	G	A	15: 8,216,382	V1413M	probably damaging	Het
2700049A03Rik	T	C	12: 71,167,150	I717T	possibly damaging	Het
3632451O06Rik	A	G	14: 49,773,786	S155P	probably benign	Het
6430571L13Rik	A	G	9: 107,346,184		probably benign	Het
Abca15	T	A	7: 120,350,903		probably benign	Het
Abca6	A	G	11: 110,219,604	V573A	possibly damaging	Het
Adgrl2	A	G	3: 148,852,863		probably benign	Het
Ahrr	G	A	13: 74,283,024		probably benign	Het
Akr1c20	T	C	13: 4,523,296	T7A	probably benign	Het
Ankrd26	A	G	6: 118,540,484	S459P	probably benign	Het
Ascc3	T	A	10: 50,842,127		probably null	Het
Brd1	T	C	15: 88,729,777	N305S	probably damaging	Het
Catip	T	A	1: 74,368,469	L320Q	possibly damaging	Het
Cttnbp2	G	A	6: 18,435,410	Q150*	probably null	Het
Cyp2d22	T	G	15: 82,373,280	N228T	probably benign	Het
Dapk1	T	C	13: 60,761,593	V1340A	probably benign	Het
Dcaf4	G	A	12: 83,535,988		probably benign	Het
Ddhd1	G	A	14: 45,595,592	T849M	probably damaging	Het
Dnah6	A	G	6: 73,021,323	S3987P	probably benign	Het
Dst	C	A	1: 34,154,646		probably benign	Het
Epha2	T	C	4: 141,321,892		probably null	Het
Ern2	T	C	7: 122,179,779	T281A	probably benign	Het
Extl1	A	G	4: 134,357,703	F652S	probably damaging	Het
Gckr	A	G	5: 31,326,948	S541G	possibly damaging	Het
Gdap1l1	A	G	2: 163,451,499		probably null	Het
Gm7535	T	C	17: 17,911,175		probably benign	Het
Gmps	T	A	3: 63,993,954	I398N	probably damaging	Het
Igf2r	A	G	17: 12,698,527	V1556A	probably benign	Het
Il3ra	T	A	14: 14,350,967	N283K	probably benign	Het
Ist1	A	G	8: 109,675,366		probably benign	Het
Lama3	A	T	18: 12,524,810	I1934F	probably damaging	Het
Lars	A	T	18: 42,202,697	M1118K	possibly damaging	Het
Lpin2	C	T	17: 71,246,519	S846L	probably damaging	Het
Lrrc4b	C	A	7: 44,462,315	T537K	probably damaging	Het
Ltn1	G	A	16: 87,405,519		probably benign	Het
Meiob	A	G	17: 24,835,161	T401A	probably benign	Het
Mettl21e	G	A	1: 44,211,123	T41M	probably damaging	Het
Miga1	C	T	3: 152,290,843	E323K	probably damaging	Het
Ndufs1	A	T	1: 63,159,748		probably null	Het
Olfr486	T	C	7: 108,172,675	D23G	probably benign	Het
Otog	G	A	7: 46,304,231	V2638M	probably damaging	Het
Parp6	T	C	9: 59,632,925	Y274H	probably damaging	Het
Prom2	A	T	2: 127,539,514		probably benign	Het
Prune2	T	A	19: 17,122,610	M1826K	probably benign	Het
Qk	T	A	17: 10,238,963	D159V	probably damaging	Het
Rab12	A	T	17: 66,500,317	I139N	probably damaging	Het
Rab25	T	A	3: 88,548,055	E7D	probably benign	Het
Rala	A	T	13: 17,888,589	V139E	probably benign	Het
Ralgapa2	A	G	2: 146,388,487		probably benign	Het
Rbl2	T	A	8: 91,074,176	Y89N	probably damaging	Het
Rho	A	T	6: 115,932,227	I75F	probably damaging	Het
Slc38a4	C	A	15: 97,008,949	A303S	probably benign	Het
Slc6a15	A	G	10: 103,409,809	D551G	probably null	Het
Smyd3	T	C	1: 179,043,872	N314S	probably benign	Het
Speer4f1	T	A	5: 17,479,514	L180*	probably null	Het
Stat6	T	C	10: 127,657,227	V576A	probably damaging	Het
Strn	T	C	17: 78,677,374	D127G	possibly damaging	Het
Syne1	T	C	10: 5,033,096	R8610G	probably benign	Het
Tbc1d7	A	C	13: 43,153,202		probably null	Het
Tcf3	C	T	10: 80,412,997	R548Q	probably damaging	Het
Tlr9	C	A	9: 106,226,087	A859D	probably benign	Het
Tmem106c	T	A	15: 97,968,139		probably benign	Het
Tmprss11c	A	T	5: 86,231,927		probably benign	Het
Tnfsf18	A	G	1: 161,494,731	R7G	probably benign	Het
Tnrc6b	T	A	15: 80,858,670		probably null	Het
Trpm7	A	T	2: 126,797,513	F1684I	probably damaging	Het
Ttbk1	C	A	17: 46,478,938	R133L	possibly damaging	Het
Ttn	A	G	2: 76,721,342	S22962P	probably damaging	Het
Ube2q1	T	A	3: 89,776,153	L135Q	probably damaging	Het
Vmn1r28	G	A	6: 58,265,717	A182T	probably benign	Het
Vwce	T	C	19: 10,659,973		probably benign	Het
Wdhd1	A	G	14: 47,267,068	S350P	probably benign	Het
Zbtb21	A	G	16: 97,951,404	S560P	probably damaging	Het

Other mutations in Agap3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00574:Agap3	APN	5	24498109	missense	probably damaging	0.99
IGL00900:Agap3	APN	5	24476368	splice site	probably benign
IGL00966:Agap3	APN	5	24501002	splice site	probably benign
IGL02207:Agap3	APN	5	24499936	missense	probably benign
IGL02431:Agap3	APN	5	24501012	missense	probably damaging	1.00
IGL02601:Agap3	APN	5	24483371	missense	possibly damaging	0.67
IGL03090:Agap3	APN	5	24501206	missense	possibly damaging	0.91
IGL03131:Agap3	APN	5	24477132	missense	probably benign	0.16
IGL03247:Agap3	APN	5	24487822	missense	probably damaging	1.00
R0344:Agap3	UTSW	5	24451202	unclassified	probably benign
R0496:Agap3	UTSW	5	24501243	missense	probably damaging	1.00
R0542:Agap3	UTSW	5	24500186	missense	possibly damaging	0.95
R1427:Agap3	UTSW	5	24476693	missense	probably benign	0.03
R1840:Agap3	UTSW	5	24500231	missense	probably damaging	1.00
R1903:Agap3	UTSW	5	24493013	missense	probably damaging	1.00
R2101:Agap3	UTSW	5	24487799	missense	probably damaging	1.00
R4601:Agap3	UTSW	5	24476408	missense	probably damaging	1.00
R4745:Agap3	UTSW	5	24451125	splice site	probably null
R4807:Agap3	UTSW	5	24477116	missense	probably damaging	1.00
R4808:Agap3	UTSW	5	24501245	missense	probably benign
R4916:Agap3	UTSW	5	24478013	missense	probably damaging	0.98
R5056:Agap3	UTSW	5	24477862	missense	probably damaging	1.00
R5094:Agap3	UTSW	5	24451321	unclassified	probably benign
R5646:Agap3	UTSW	5	24483397	missense	probably benign	0.01
R5937:Agap3	UTSW	5	24477817	missense	probably damaging	0.99
R6365:Agap3	UTSW	5	24474985	missense	probably benign	0.43
R6798:Agap3	UTSW	5	24498282	splice site	probably null
R6802:Agap3	UTSW	5	24487793	missense	possibly damaging	0.87
R6863:Agap3	UTSW	5	24452463	missense	possibly damaging	0.63
R6863:Agap3	UTSW	5	24452464	nonsense	probably null
R7039:Agap3	UTSW	5	24483401	missense	probably benign	0.01
R7111:Agap3	UTSW	5	24501398	missense	probably damaging	1.00
R7313:Agap3	UTSW	5	24452384	missense	probably benign	0.25
R7791:Agap3	UTSW	5	24476413	missense	probably damaging	1.00
R8124:Agap3	UTSW	5	24478130	missense	probably benign	0.02
R8293:Agap3	UTSW	5	24487885	missense	probably damaging	1.00
R8907:Agap3	UTSW	5	24474631	missense	probably benign
R9127:Agap3	UTSW	5	24476441	splice site	probably benign
R9694:Agap3	UTSW	5	24477141	missense	probably benign	0.02

Predicted Primers

PCR Primer
(F):5'- CCCATGATAGCACCTTTATGGCCC -3'
(R):5'- AGCCCTGTGTGTCTAAGTGTGAGAG -3'

Sequencing Primer
(F):5'- ATAGCACCTTTATGGCCCTTCTG -3'
(R):5'- GAGAGAGATTGCATCCTCTTGACC -3'

Posted On

2013-04-16