Mutagenetix > Incidental Mutation

Incidental Mutation 'R4395:Iqsec2'

325470

Institutional Source

Beutler Lab

Gene Symbol

Iqsec2

Ensembl Gene

ENSMUSG00000041115

Gene Name

IQ motif and Sec7 domain 2

Synonyms

MMRRC Submission

041684-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.401) question?

Stock #

R4395 (G1)

Quality Score

222

Status

Not validated

Chromosome

Chromosomal Location

150927193-151008232 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 150992049 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 562 (T562I)

Ref Sequence

ENSEMBL: ENSMUSP00000127249 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000096275] [ENSMUST00000112604] [ENSMUST00000112605] [ENSMUST00000168786]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000096275
AA Change: T357I

PolyPhen 2 Score 0.355 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000093995
Gene: ENSMUSG00000041115
AA Change: T357I

Domain	Start	End	E-Value	Type
low complexity region	164	177	N/A	INTRINSIC
low complexity region	228	246	N/A	INTRINSIC
low complexity region	309	334	N/A	INTRINSIC
low complexity region	343	355	N/A	INTRINSIC
low complexity region	395	410	N/A	INTRINSIC
low complexity region	444	461	N/A	INTRINSIC
low complexity region	491	515	N/A	INTRINSIC
Sec7	545	736	2.19e-88	SMART
PH	767	878	6.87e-3	SMART
Blast:Sec7	886	931	3e-18	BLAST
low complexity region	932	946	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000112604
AA Change: T562I

PolyPhen 2 Score 0.947 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000108223
Gene: ENSMUSG00000041115
AA Change: T562I

Domain	Start	End	E-Value	Type
low complexity region	4	16	N/A	INTRINSIC
coiled coil region	23	74	N/A	INTRINSIC
low complexity region	167	174	N/A	INTRINSIC
low complexity region	206	232	N/A	INTRINSIC
low complexity region	369	382	N/A	INTRINSIC
low complexity region	433	451	N/A	INTRINSIC
low complexity region	514	539	N/A	INTRINSIC
low complexity region	548	560	N/A	INTRINSIC
low complexity region	600	615	N/A	INTRINSIC
low complexity region	649	666	N/A	INTRINSIC
low complexity region	696	720	N/A	INTRINSIC
Sec7	750	941	2.19e-88	SMART
PH	972	1083	6.87e-3	SMART
Blast:Sec7	1091	1136	3e-18	BLAST
low complexity region	1137	1151	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000112605
AA Change: T562I

PolyPhen 2 Score 0.486 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000108224
Gene: ENSMUSG00000041115
AA Change: T562I

Domain	Start	End	E-Value	Type
low complexity region	4	16	N/A	INTRINSIC
coiled coil region	23	74	N/A	INTRINSIC
low complexity region	167	174	N/A	INTRINSIC
low complexity region	206	232	N/A	INTRINSIC
low complexity region	369	382	N/A	INTRINSIC
low complexity region	433	451	N/A	INTRINSIC
low complexity region	514	539	N/A	INTRINSIC
low complexity region	548	560	N/A	INTRINSIC
low complexity region	600	615	N/A	INTRINSIC
low complexity region	649	666	N/A	INTRINSIC
low complexity region	696	720	N/A	INTRINSIC
Sec7	750	941	2.19e-88	SMART
PH	972	1083	6.87e-3	SMART
Blast:Sec7	1091	1136	4e-18	BLAST
low complexity region	1137	1151	N/A	INTRINSIC
low complexity region	1201	1211	N/A	INTRINSIC
low complexity region	1228	1253	N/A	INTRINSIC
low complexity region	1273	1318	N/A	INTRINSIC
low complexity region	1337	1349	N/A	INTRINSIC
low complexity region	1392	1462	N/A	INTRINSIC
low complexity region	1470	1482	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000168786
AA Change: T562I

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000127249
Gene: ENSMUSG00000041115
AA Change: T562I

Domain	Start	End	E-Value	Type
low complexity region	4	16	N/A	INTRINSIC
coiled coil region	23	74	N/A	INTRINSIC
low complexity region	167	174	N/A	INTRINSIC
low complexity region	206	232	N/A	INTRINSIC
low complexity region	369	382	N/A	INTRINSIC
low complexity region	433	451	N/A	INTRINSIC
low complexity region	514	539	N/A	INTRINSIC
low complexity region	548	560	N/A	INTRINSIC
low complexity region	600	615	N/A	INTRINSIC
low complexity region	649	666	N/A	INTRINSIC
low complexity region	696	720	N/A	INTRINSIC
Sec7	750	941	2.19e-88	SMART
Blast:PH	972	1074	7e-61	BLAST
Blast:Sec7	1082	1127	4e-18	BLAST
low complexity region	1128	1142	N/A	INTRINSIC
low complexity region	1192	1202	N/A	INTRINSIC
low complexity region	1219	1244	N/A	INTRINSIC
low complexity region	1264	1309	N/A	INTRINSIC
low complexity region	1328	1340	N/A	INTRINSIC
low complexity region	1383	1453	N/A	INTRINSIC
low complexity region	1461	1473	N/A	INTRINSIC

Meta Mutation Damage Score

0.0684

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.8%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a guanine nucleotide exchange factor for the ARF family of small GTP-binding proteins. The encoded protein is a component of the postsynaptic density at excitatory synapses, and may play a critical role in cytoskeletal and synaptic organization through the activation of selected ARF substrates including ARF1 and ARF6. Mutations in this gene have been implicated in nonsyndromic X-linked mental retardation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2011]

Allele List at MGI

Other mutations in this stock

Total: 42 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acnat1	A	G	4: 49,447,679 (GRCm39)	Y283H	probably benign	Het
Adamtsl5	A	G	10: 80,180,736 (GRCm39)	C109R	probably damaging	Het
Adgrg4	T	G	X: 55,977,703 (GRCm39)	L2193V	probably damaging	Het
Alpk3	C	T	7: 80,744,703 (GRCm39)	S1266F	probably damaging	Het
Arfgef3	A	G	10: 18,473,457 (GRCm39)	L1614P	probably damaging	Het
Atm	T	C	9: 53,376,527 (GRCm39)	R2038G	probably benign	Het
Bahd1	G	A	2: 118,753,004 (GRCm39)	R757H	probably damaging	Het
Capza2	T	C	6: 17,656,449 (GRCm39)		probably null	Het
Cfap43	T	C	19: 47,740,352 (GRCm39)	T1274A	probably benign	Het
Chil4	G	A	3: 106,111,043 (GRCm39)	P284S	possibly damaging	Het
Cisd3	A	G	11: 97,579,212 (GRCm39)	Y115C	probably damaging	Het
Crebl2	A	G	6: 134,826,208 (GRCm39)	E53G	probably damaging	Het
Ech1	T	C	7: 28,525,671 (GRCm39)	S107P	probably damaging	Het
Fam3b	C	A	16: 97,282,986 (GRCm39)		probably null	Het
Fat1	T	A	8: 45,405,383 (GRCm39)	N711K	probably damaging	Het
Grm8	T	A	6: 27,429,431 (GRCm39)	I488F	probably damaging	Het
Hmga2	C	T	10: 120,311,956 (GRCm39)	G5S	probably damaging	Het
Homer3	G	A	8: 70,742,793 (GRCm39)		probably null	Het
Ifit3b	G	T	19: 34,589,951 (GRCm39)	E376*	probably null	Het
Ints5	A	G	19: 8,873,808 (GRCm39)	E589G	probably damaging	Het
Lamc3	A	G	2: 31,821,964 (GRCm39)	E1304G	probably benign	Het
Ltv1	T	C	10: 13,066,323 (GRCm39)	Y101C	probably benign	Het
Maf1	T	C	15: 76,236,357 (GRCm39)		probably benign	Het
Map3k13	A	T	16: 21,717,321 (GRCm39)	K185N	possibly damaging	Het
Mtcl3	T	C	10: 29,023,351 (GRCm39)	S233P	probably benign	Het
Mtus2	A	T	5: 148,013,432 (GRCm39)	Q75L	probably benign	Het
Nod2	T	A	8: 89,391,019 (GRCm39)	F427Y	probably damaging	Het
Or1s2	A	T	19: 13,758,275 (GRCm39)	I100F	probably benign	Het
Or5p51	A	G	7: 107,444,469 (GRCm39)	L157P	probably damaging	Het
Pik3cg	T	C	12: 32,254,091 (GRCm39)	D632G	probably damaging	Het
Plekhs1	A	G	19: 56,468,326 (GRCm39)	D298G	probably benign	Het
Rbm34	T	C	8: 127,676,131 (GRCm39)	T375A	probably benign	Het
Slc4a7	C	T	14: 14,765,665 (GRCm38)	T549I	probably damaging	Het
Slco1a7	T	C	6: 141,657,844 (GRCm39)	I565V	probably benign	Het
Stk17b	A	G	1: 53,803,274 (GRCm39)	I47T	probably damaging	Het
Tenm2	C	T	11: 35,915,451 (GRCm39)	V2028I	probably benign	Het
Tle4	A	T	19: 14,495,302 (GRCm39)	H142Q	probably benign	Het
Tns2	C	T	15: 102,017,369 (GRCm39)	R281C	probably damaging	Het
Tnxb	C	T	17: 34,897,636 (GRCm39)	Q804*	probably null	Het
Trpm2	T	C	10: 77,765,053 (GRCm39)	I983V	probably benign	Het
Ttll8	C	T	15: 88,799,783 (GRCm39)	A553T	possibly damaging	Het
Ubxn11	G	T	4: 133,843,431 (GRCm39)	E171D	possibly damaging	Het

Other mutations in Iqsec2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0193:Iqsec2	UTSW	X	151,006,399 (GRCm39)	missense	probably benign	0.33
R0675:Iqsec2	UTSW	X	150,987,120 (GRCm39)	missense	possibly damaging	0.76
R1169:Iqsec2	UTSW	X	150,927,727 (GRCm39)	missense	probably benign	0.01
R1171:Iqsec2	UTSW	X	150,927,727 (GRCm39)	missense	probably benign	0.01
R4397:Iqsec2	UTSW	X	150,992,049 (GRCm39)	missense	probably damaging	0.98
R4553:Iqsec2	UTSW	X	150,994,277 (GRCm39)	missense	probably benign	0.03
X0026:Iqsec2	UTSW	X	150,992,646 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATCAGGGCCTATGTCTGAGG -3'
(R):5'- TCAGCCTCATACACCAGCTG -3'

Sequencing Primer
(F):5'- CTATGTCTGAGGAGCCAGGGTC -3'
(R):5'- TCATACACCAGCTGGCGGTG -3'

Posted On

2015-07-06