Mutagenetix > Incidental Mutation

Incidental Mutation 'R2131:Depdc5'

228058

Institutional Source

Beutler Lab

Gene Symbol

Depdc5

Ensembl Gene

ENSMUSG00000037426

Gene Name

DEP domain containing 5

Synonyms

MMRRC Submission

040134-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R2131 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

32863701-32994236 bp(+) (GRCm38)

Type of Mutation

nonsense

DNA Base Change (assembly)

T to A at 32990781 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Stop codon at position 1469 (L1469*)

Ref Sequence

ENSEMBL: ENSMUSP00000085207 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000087897] [ENSMUST00000119705] [ENSMUST00000120902] [ENSMUST00000124780]

AlphaFold

P61460

Predicted Effect

probably null
Transcript: ENSMUST00000087897
AA Change: L1469*

SMART Domains

Protein: ENSMUSP00000085207
Gene: ENSMUSG00000037426
AA Change: L1469*

Domain	Start	End	E-Value	Type
Pfam:DUF3608	100	382	2.3e-63	PFAM
low complexity region	491	508	N/A	INTRINSIC
low complexity region	656	667	N/A	INTRINSIC
low complexity region	690	699	N/A	INTRINSIC
low complexity region	826	836	N/A	INTRINSIC
low complexity region	994	1006	N/A	INTRINSIC
low complexity region	1159	1175	N/A	INTRINSIC
DEP	1184	1259	2.49e-15	SMART
low complexity region	1322	1335	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000119705
AA Change: F1480L

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000113862
Gene: ENSMUSG00000037426
AA Change: F1480L

Domain	Start	End	E-Value	Type
Pfam:DUF3608	100	382	3e-117	PFAM
low complexity region	491	508	N/A	INTRINSIC
low complexity region	656	667	N/A	INTRINSIC
low complexity region	690	699	N/A	INTRINSIC
low complexity region	817	827	N/A	INTRINSIC
low complexity region	985	997	N/A	INTRINSIC
low complexity region	1150	1166	N/A	INTRINSIC
DEP	1175	1250	2.49e-15	SMART
low complexity region	1313	1326	N/A	INTRINSIC
low complexity region	1511	1525	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000120902
AA Change: F1458L

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000113980
Gene: ENSMUSG00000037426
AA Change: F1458L

Domain	Start	End	E-Value	Type
Pfam:DUF3608	100	382	3.7e-63	PFAM
low complexity region	491	508	N/A	INTRINSIC
low complexity region	656	667	N/A	INTRINSIC
low complexity region	690	699	N/A	INTRINSIC
low complexity region	817	827	N/A	INTRINSIC
low complexity region	985	997	N/A	INTRINSIC
low complexity region	1128	1144	N/A	INTRINSIC
DEP	1153	1228	2.49e-15	SMART
low complexity region	1291	1304	N/A	INTRINSIC
low complexity region	1489	1503	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000124780

SMART Domains

Protein: ENSMUSP00000120120
Gene: ENSMUSG00000037426

Domain	Start	End	E-Value	Type
low complexity region	179	189	N/A	INTRINSIC
low complexity region	347	359	N/A	INTRINSIC
SCOP:d1fsha_	519	586	1e-13	SMART
Blast:DEP	537	589	2e-24	BLAST

Predicted Effect

unknown
Transcript: ENSMUST00000137169
AA Change: F864L

SMART Domains

Protein: ENSMUSP00000121089
Gene: ENSMUSG00000037426
AA Change: F864L

Domain	Start	End	E-Value	Type
low complexity region	54	65	N/A	INTRINSIC
low complexity region	88	97	N/A	INTRINSIC
low complexity region	224	234	N/A	INTRINSIC
low complexity region	392	404	N/A	INTRINSIC
low complexity region	535	551	N/A	INTRINSIC
DEP	560	635	2.49e-15	SMART
low complexity region	698	711	N/A	INTRINSIC
low complexity region	896	910	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196072

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.0%

Validation Efficiency

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 IML1 family of proteins involved in G-protein signaling pathways. The mechanistic target of rapamycin complex 1 (mTORC1) pathway regulates cell growth by sensing the availability of nutrients. The protein encoded by this gene is a component of the GATOR1 (GAP activity toward Rags) complex which inhibits the amino acid-sensing branch of the mTORC1 pathway. Mutations in this gene are associated with autosomal dominant familial focal epilepsy with variable foci. A single nucleotide polymorphism in an intron of this gene has been associated with an increased risk of hepatocellular carcinoma in individuals with chronic hepatitis C virus infection. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit preweaning lethality. Mice homozygous for a conditional allele activated in neurons exhibit reduced body weight, limb grasping, premature death, spontaneous seizure, increased brain size due to neuron hypertrophy and increased PTZ seizure susceptibility. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 123 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010111I01Rik	T	A	13: 63,210,149	C656S	probably benign	Het
4931408C20Rik	T	C	1: 26,685,854	R82G	probably benign	Het
9030624J02Rik	T	C	7: 118,794,575	Y516H	probably damaging	Het
A2ml1	T	A	6: 128,576,260	N178I	probably damaging	Het
Acvr2b	A	G	9: 119,432,808	R437G	probably damaging	Het
Adamtsl3	C	A	7: 82,578,594	A1329E	probably damaging	Het
Adgrl2	T	C	3: 148,890,488	I71V	probably damaging	Het
Adra1a	A	T	14: 66,727,532	I324F	possibly damaging	Het
Akap13	G	T	7: 75,611,434	A1269S	probably benign	Het
Ampd1	G	T	3: 103,094,878		probably null	Het
Ankrd16	T	A	2: 11,783,695	D211E	probably damaging	Het
Aox3	A	G	1: 58,169,843	H845R	probably damaging	Het
Apc	C	A	18: 34,312,045	Q665K	possibly damaging	Het
Arap2	T	C	5: 62,677,958	N747S	probably damaging	Het
Arsk	A	T	13: 76,091,812	C47*	probably null	Het
Atp8b5	T	A	4: 43,370,726	F1001I	probably benign	Het
Bap1	T	A	14: 31,258,331	Y645*	probably null	Het
Brca2	A	G	5: 150,557,129	Y2760C	probably damaging	Het
Cad	T	A	5: 31,058,072	F76I	probably damaging	Het
Capn9	G	A	8: 124,605,711	G430R	possibly damaging	Het
Ccdc27	TTCCTCCTCCTCCTCCTCCTC	TTCCTCCTCCTCCTCCTC	4: 154,036,306		probably benign	Het
Cdkn2c	A	C	4: 109,665,063	N28K	probably null	Het
Celsr1	T	A	15: 85,963,223	I1438F	probably benign	Het
Cfhr2	T	G	1: 139,831,155	R52S	probably benign	Het
Cldn1	G	C	16: 26,371,550	A26G	probably damaging	Het
Col20a1	T	A	2: 180,992,573	F110L	probably damaging	Het
Creg2	T	C	1: 39,624,978	N204S	probably benign	Het
Cx3cl1	C	A	8: 94,779,573	Q69K	probably benign	Het
Cyfip2	T	C	11: 46,286,131	E74G	possibly damaging	Het
Cyp2g1	A	T	7: 26,820,710	I456F	probably damaging	Het
Dapk1	A	G	13: 60,729,531	E528G	possibly damaging	Het
Dapk1	T	A	13: 60,761,667	W1365R	possibly damaging	Het
Dbt	T	A	3: 116,539,124	D16E	probably damaging	Het
Dnah3	T	A	7: 119,967,759	T2415S	possibly damaging	Het
Dnmbp	A	G	19: 43,854,311	L1210S	probably damaging	Het
Dpyd	T	C	3: 118,674,568	V77A	probably benign	Het
Eps15l1	A	T	8: 72,386,868	V260D	probably benign	Het
Eya1	A	G	1: 14,170,974	V573A	probably benign	Het
Fam171b	T	A	2: 83,879,858	S625T	probably damaging	Het
Fam186a	T	C	15: 99,933,676		probably benign	Het
Fam208a	A	G	14: 27,476,614	N1301S	possibly damaging	Het
Gabra4	G	T	5: 71,641,224	D137E	probably benign	Het
Gatsl2	G	A	5: 134,136,153	C187Y	probably damaging	Het
Gemin4	G	C	11: 76,211,050	P962A	probably damaging	Het
Gm43302	T	C	5: 105,274,744	D474G	probably damaging	Het
Golim4	A	T	3: 75,908,149	V116D	probably damaging	Het
Gpr19	T	C	6: 134,870,442	M1V	probably null	Het
Hnf4a	T	A	2: 163,547,418	N29K	probably benign	Het
Htt	A	G	5: 34,877,109	R1975G	possibly damaging	Het
Ift20	G	A	11: 78,540,034	E68K	probably damaging	Het
Il4i1	G	A	7: 44,840,070	V420M	probably damaging	Het
Insrr	G	A	3: 87,810,572		probably null	Het
Ipo9	ATCCTCCTCCTCCTCCTC	ATCCTCCTCCTCCTCCTCCTC	1: 135,386,268		probably benign	Het
Ipo9	A	G	1: 135,402,250	V484A	probably benign	Het
Jmjd4	A	T	11: 59,454,955	H287L	probably damaging	Het
Kcnj13	A	G	1: 87,386,534	V322A	probably benign	Het
Kdm5d	T	C	Y: 941,483	L1228P	probably benign	Het
Klra3	A	G	6: 130,335,775	S9P	probably benign	Het
Ldhd	C	T	8: 111,628,537		probably null	Het
Lmo2	T	C	2: 103,981,062	Y147H	probably damaging	Het
Lmo7	A	T	14: 101,900,238	D670V	probably damaging	Het
Lmtk2	C	T	5: 144,174,988	T842I	possibly damaging	Het
Lrp5	T	C	19: 3,622,708	T534A	possibly damaging	Het
Lrrc24	A	T	15: 76,715,581	F453I	possibly damaging	Het
Magel2	A	T	7: 62,377,738	H130L	unknown	Het
Mcpt8	T	C	14: 56,082,283	I237V	probably damaging	Het
Med4	A	G	14: 73,517,996	N248S	possibly damaging	Het
Mest	C	T	6: 30,745,885	L269F	probably damaging	Het
Mib2	C	T	4: 155,655,238		probably null	Het
Mki67	T	A	7: 135,704,241		probably null	Het
Mnx1	T	A	5: 29,474,189	S299C	unknown	Het
Nbr1	T	A	11: 101,566,191		probably null	Het
Ncapd3	T	G	9: 27,083,346	V1174G	probably damaging	Het
Nyap1	A	C	5: 137,733,681		probably null	Het
Olfml3	T	A	3: 103,735,869	M399L	probably benign	Het
Olfr341	A	G	2: 36,480,047	S28P	possibly damaging	Het
Olfr775	T	C	10: 129,251,074	F180S	probably benign	Het
Oosp1	T	C	19: 11,690,950	D23G	probably damaging	Het
Optc	A	T	1: 133,903,796		probably null	Het
Osbpl6	T	A	2: 76,586,214	I546K	probably damaging	Het
Otog	A	T	7: 46,250,100	N275I	probably damaging	Het
Pcdhb14	C	A	18: 37,447,870	Q10K	probably benign	Het
Pcx	T	C	19: 4,602,551	F189L	probably benign	Het
Pde6b	A	G	5: 108,428,203	D718G	probably damaging	Het
Pklr	C	A	3: 89,142,660	P314Q	probably damaging	Het
Plcb1	T	A	2: 135,325,667	Y460*	probably null	Het
Plekha6	C	A	1: 133,279,365		probably null	Het
Plekho1	A	G	3: 95,989,117	S347P	probably damaging	Het
Plxna2	G	A	1: 194,644,750	D331N	probably benign	Het
Prelp	C	T	1: 133,915,131	R92K	probably benign	Het
Prkra	A	T	2: 76,647,136	I75K	probably damaging	Het
Ptpn11	G	A	5: 121,172,026	A31V	probably damaging	Het
Pzp	T	C	6: 128,491,161		probably null	Het
Rbm12	A	T	2: 156,095,510	C947*	probably null	Het
Ren1	C	G	1: 133,350,778		probably null	Het
Sarm1	A	T	11: 78,475,307	C649S	probably benign	Het
Sept12	T	A	16: 4,991,779	Q223L	probably damaging	Het
Sept4	A	T	11: 87,583,436	Q60L	probably benign	Het
Slc22a21	A	T	11: 53,979,733	L42Q	probably damaging	Het
Slc44a1	GCCC	GCCCCCCC	4: 53,563,246		probably null	Het
Slc9a4	T	G	1: 40,607,741		probably null	Het
Sort1	T	A	3: 108,351,686	F678Y	probably benign	Het
Spag6	T	A	2: 18,733,097	C259*	probably null	Het
Stard13	T	C	5: 151,045,168	Y879C	probably damaging	Het
Stk24	A	T	14: 121,302,211	I191N	probably damaging	Het
Tacc1	A	T	8: 25,164,493	N271K	probably damaging	Het
Tacc2	T	A	7: 130,621,857	S91T	possibly damaging	Het
Tacr3	T	C	3: 134,932,180	V366A	probably benign	Het
Tbccd1	A	G	16: 22,841,989	S26P	probably benign	Het
Tecpr1	T	A	5: 144,208,645	T595S	probably benign	Het
Tjp3	T	A	10: 81,278,054	M457L	possibly damaging	Het
Tor1aip2	A	G	1: 156,065,349	Y467C	probably damaging	Het
Trove2	T	C	1: 143,760,034	D458G	probably benign	Het
Ttc9b	T	A	7: 27,654,349		probably null	Het
Tti1	T	C	2: 158,000,743	R789G	probably benign	Het
Ttn	A	T	2: 76,832,217		probably null	Het
Txk	T	A	5: 72,696,579	T472S	probably damaging	Het
Ube2cbp	A	T	9: 86,372,487		probably null	Het
Vav2	C	A	2: 27,299,396	R176L	possibly damaging	Het
Wdr27	T	A	17: 14,928,332	D133V	probably damaging	Het
Zc3h7a	A	T	16: 11,150,605	Y503*	probably null	Het
Zdhhc13	T	A	7: 48,824,644	L548Q	possibly damaging	Het
Zfp467	A	C	6: 48,442,661	S38A	probably damaging	Het

Other mutations in Depdc5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00861:Depdc5	APN	5	32967814	splice site	probably null
IGL01019:Depdc5	APN	5	32893401	missense	probably damaging	0.96
IGL01067:Depdc5	APN	5	32899067	splice site	probably null
IGL01405:Depdc5	APN	5	32937689	missense	possibly damaging	0.90
IGL01577:Depdc5	APN	5	32955897	missense	possibly damaging	0.49
IGL01633:Depdc5	APN	5	32924200	missense	probably damaging	1.00
IGL01998:Depdc5	APN	5	32945151	splice site	probably benign
IGL02025:Depdc5	APN	5	32946632	critical splice acceptor site	probably null
IGL02167:Depdc5	APN	5	32903801	missense	probably damaging	1.00
IGL02537:Depdc5	APN	5	32967787	missense	probably damaging	1.00
IGL02812:Depdc5	APN	5	32893368	splice site	probably benign
IGL03001:Depdc5	APN	5	32945090	missense	possibly damaging	0.74
IGL03253:Depdc5	APN	5	32868813	unclassified	probably benign
alligator	UTSW	5	32964507	splice site	probably null
lagarto	UTSW	5	32979508	missense	probably damaging	1.00
sauros	UTSW	5	32986966	missense	possibly damaging	0.92
IGL02988:Depdc5	UTSW	5	32956167	splice site	probably null
R0038:Depdc5	UTSW	5	32868853	missense	probably benign	0.01
R0038:Depdc5	UTSW	5	32868853	missense	probably benign	0.01
R0153:Depdc5	UTSW	5	32933937	splice site	probably benign
R0179:Depdc5	UTSW	5	32901574	unclassified	probably benign
R0212:Depdc5	UTSW	5	32912242	missense	probably benign	0.00
R0239:Depdc5	UTSW	5	32943240	missense	probably damaging	1.00
R0239:Depdc5	UTSW	5	32943240	missense	probably damaging	1.00
R0302:Depdc5	UTSW	5	32904546	critical splice donor site	probably benign
R0511:Depdc5	UTSW	5	32945028	nonsense	probably null
R0677:Depdc5	UTSW	5	32901470	missense	probably damaging	1.00
R0884:Depdc5	UTSW	5	32917978	missense	possibly damaging	0.94
R0973:Depdc5	UTSW	5	32986966	missense	possibly damaging	0.92
R1314:Depdc5	UTSW	5	32877074	missense	probably damaging	1.00
R1611:Depdc5	UTSW	5	32990953	missense	probably damaging	1.00
R1687:Depdc5	UTSW	5	32910407	critical splice acceptor site	probably benign
R1748:Depdc5	UTSW	5	32917942	missense	probably benign	0.24
R1903:Depdc5	UTSW	5	32910407	critical splice acceptor site	probably benign
R1956:Depdc5	UTSW	5	32903831	missense	probably damaging	1.00
R1997:Depdc5	UTSW	5	32901906	critical splice donor site	probably null
R2079:Depdc5	UTSW	5	32946674	missense	possibly damaging	0.75
R2291:Depdc5	UTSW	5	32979402	missense	probably damaging	1.00
R2422:Depdc5	UTSW	5	32991035	missense	probably damaging	1.00
R2851:Depdc5	UTSW	5	32924171	missense	probably damaging	0.96
R2852:Depdc5	UTSW	5	32924171	missense	probably damaging	0.96
R2937:Depdc5	UTSW	5	32901621	splice site	probably null
R2938:Depdc5	UTSW	5	32901621	splice site	probably null
R2974:Depdc5	UTSW	5	32934017	critical splice donor site	probably null
R3884:Depdc5	UTSW	5	32944077	missense	probably damaging	1.00
R3967:Depdc5	UTSW	5	32944115	nonsense	probably null
R4118:Depdc5	UTSW	5	32964635	missense	probably damaging	1.00
R4197:Depdc5	UTSW	5	32991203	missense	possibly damaging	0.93
R4407:Depdc5	UTSW	5	32904534	critical splice donor site	probably null
R4534:Depdc5	UTSW	5	32910407	critical splice acceptor site	probably benign
R4535:Depdc5	UTSW	5	32910407	critical splice acceptor site	probably benign
R4538:Depdc5	UTSW	5	32983946	missense	probably damaging	1.00
R4613:Depdc5	UTSW	5	32975446	missense	probably damaging	1.00
R4736:Depdc5	UTSW	5	32975322	missense	probably benign
R4738:Depdc5	UTSW	5	32975322	missense	probably benign
R4765:Depdc5	UTSW	5	32937635	missense	probably damaging	1.00
R5021:Depdc5	UTSW	5	32979414	missense	probably damaging	1.00
R5259:Depdc5	UTSW	5	32938291	missense	probably damaging	1.00
R5261:Depdc5	UTSW	5	32938291	missense	probably damaging	1.00
R5541:Depdc5	UTSW	5	32864629	utr 5 prime	probably benign
R5594:Depdc5	UTSW	5	32901490	missense	possibly damaging	0.46
R5929:Depdc5	UTSW	5	32975506	nonsense	probably null
R6132:Depdc5	UTSW	5	32910467	missense	probably damaging	0.99
R6146:Depdc5	UTSW	5	32968731	missense	probably benign	0.01
R6336:Depdc5	UTSW	5	32964507	splice site	probably null
R6468:Depdc5	UTSW	5	32912231	missense	probably benign	0.02
R6911:Depdc5	UTSW	5	32924192	missense	probably damaging	1.00
R6969:Depdc5	UTSW	5	32983860	missense	probably damaging	1.00
R7002:Depdc5	UTSW	5	32877158	splice site	probably null
R7066:Depdc5	UTSW	5	32901848	missense	probably benign	0.08
R7231:Depdc5	UTSW	5	32901865	missense	possibly damaging	0.92
R7264:Depdc5	UTSW	5	32967745	missense	probably benign
R7302:Depdc5	UTSW	5	32979508	missense	probably damaging	1.00
R7386:Depdc5	UTSW	5	32927936	missense	probably benign
R7564:Depdc5	UTSW	5	32901510	missense	probably damaging	1.00
R7636:Depdc5	UTSW	5	32917983	missense	probably benign
R7795:Depdc5	UTSW	5	32944103	missense	probably damaging	1.00
R7845:Depdc5	UTSW	5	32903915	splice site	probably null
R8013:Depdc5	UTSW	5	32973842	missense	probably benign	0.01
R8037:Depdc5	UTSW	5	32959348	critical splice donor site	probably null
R8038:Depdc5	UTSW	5	32959348	critical splice donor site	probably null
R8065:Depdc5	UTSW	5	32895908	missense	possibly damaging	0.89
R8067:Depdc5	UTSW	5	32895908	missense	possibly damaging	0.89
R8108:Depdc5	UTSW	5	32945049	missense	probably benign	0.01
R8112:Depdc5	UTSW	5	32968706	missense	possibly damaging	0.67
R8213:Depdc5	UTSW	5	32937637	missense	probably damaging	1.00
R8382:Depdc5	UTSW	5	32927898	missense	probably benign	0.00
R8680:Depdc5	UTSW	5	32944038	missense	possibly damaging	0.48
R8743:Depdc5	UTSW	5	32924243	missense	probably benign	0.10
R8754:Depdc5	UTSW	5	32979537	missense	probably benign	0.00
R9157:Depdc5	UTSW	5	32945108	missense	probably damaging	0.98
R9364:Depdc5	UTSW	5	32964732	missense	probably benign
R9441:Depdc5	UTSW	5	32937698	missense	probably benign	0.03
R9450:Depdc5	UTSW	5	32934010	missense	probably benign
R9459:Depdc5	UTSW	5	32990773	missense	probably damaging	0.99
R9554:Depdc5	UTSW	5	32964732	missense	probably benign
R9569:Depdc5	UTSW	5	32867977	missense	probably damaging	0.98
X0027:Depdc5	UTSW	5	32904292	missense	probably damaging	1.00
Z1176:Depdc5	UTSW	5	32943282	missense	possibly damaging	0.87

Predicted Primers

PCR Primer
(F):5'- GCAGGCTAAACCATGAGCAG -3'
(R):5'- AACACCGTTCCTGAAGGGAG -3'

Sequencing Primer
(F):5'- TAGTGAGAACAACAATCTGTAGCCCG -3'
(R):5'- TTCCTGAAGGGAGAGACCATGC -3'

Posted On

2014-09-17