Mutagenetix > Incidental Mutation

Incidental Mutation 'R6911:Depdc5'

539015

Institutional Source

Beutler Lab

Gene Symbol

Depdc5

Ensembl Gene

ENSMUSG00000037426

Gene Name

DEP domain containing 5

Synonyms

MMRRC Submission

045003-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6911 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

32863701-32994236 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 32924192 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Leucine at position 566 (Q566L)

Ref Sequence

ENSEMBL: ENSMUSP00000113980 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000049780] [ENSMUST00000087897] [ENSMUST00000119705] [ENSMUST00000120902] [ENSMUST00000124780] [ENSMUST00000195980]

AlphaFold

P61460

Predicted Effect

probably benign
Transcript: ENSMUST00000049780
AA Change: Q566L

PolyPhen 2 Score 0.279 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000052807
Gene: ENSMUSG00000037426
AA Change: Q566L

Domain	Start	End	E-Value	Type
Pfam:DUF3608	100	382	3.7e-64	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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000087897
AA Change: Q566L

PolyPhen 2 Score 0.911 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000085207
Gene: ENSMUSG00000037426
AA Change: Q566L

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: Q566L

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000113862
Gene: ENSMUSG00000037426
AA Change: Q566L

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: Q566L

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000113980
Gene: ENSMUSG00000037426
AA Change: Q566L

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

probably benign
Transcript: ENSMUST00000137169

SMART Domains

Protein: ENSMUSP00000121089
Gene: ENSMUSG00000037426

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

probably benign
Transcript: ENSMUST00000195980

SMART Domains

Protein: ENSMUSP00000143228
Gene: ENSMUSG00000037426

Domain	Start	End	E-Value	Type
Pfam:DUF3608	100	147	4e-7	PFAM

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.1%
20x: 97.1%

Validation Efficiency

98% (60/61)

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930407I10Rik	T	A	15: 82,063,867 (GRCm38)	M655K	probably benign	Het
Adam34l	A	T	8: 43,625,109 (GRCm38)	F693I	probably benign	Het
Amt	G	T	9: 108,301,229 (GRCm38)		probably null	Het
Anapc7	A	T	5: 122,440,280 (GRCm38)	K443*	probably null	Het
Apcs	A	G	1: 172,894,185 (GRCm38)	V198A	probably benign	Het
Atp2a1	A	G	7: 126,456,836 (GRCm38)	V271A	probably damaging	Het
Bltp2	T	A	11: 78,268,353 (GRCm38)	I459N	probably damaging	Het
Cdh20	T	C	1: 104,984,686 (GRCm38)	I555T	possibly damaging	Het
Cgnl1	T	C	9: 71,656,215 (GRCm38)	E810G	possibly damaging	Het
Cntnap5c	A	G	17: 57,892,014 (GRCm38)	D101G	probably damaging	Het
Coq7	T	A	7: 118,510,162 (GRCm38)	H221L	unknown	Het
Dync1i2	G	A	2: 71,247,102 (GRCm38)	V233I	probably benign	Het
Erp44	G	T	4: 48,204,268 (GRCm38)	H298N	probably benign	Het
Fam162a	A	G	16: 36,046,377 (GRCm38)		probably null	Het
Fancd2	A	G	6: 113,548,385 (GRCm38)	E274G	probably damaging	Het
Fkbp15	G	T	4: 62,340,290 (GRCm38)	Q147K	probably damaging	Het
Ganab	T	A	19: 8,907,788 (GRCm38)		probably null	Het
Gfm1	T	C	3: 67,451,303 (GRCm38)	V409A	possibly damaging	Het
Gnptab	G	A	10: 88,431,396 (GRCm38)	G450S	probably damaging	Het
Gpatch2l	G	A	12: 86,244,184 (GRCm38)	R47H	probably damaging	Het
Grid1	A	T	14: 34,820,228 (GRCm38)	M1L	probably benign	Het
Helz	C	T	11: 107,619,225 (GRCm38)	T558I	probably benign	Het
Htra4	A	G	8: 25,025,705 (GRCm38)	V439A	probably damaging	Het
Kctd17	A	G	15: 78,434,006 (GRCm38)	E95G	probably damaging	Het
Kif18b	T	C	11: 102,916,380 (GRCm38)	D43G	probably damaging	Het
Lrpprc	G	A	17: 84,756,283 (GRCm38)	S550L	possibly damaging	Het
Lrrfip1	T	A	1: 91,114,807 (GRCm38)	C311*	probably null	Het
Mcoln2	C	T	3: 146,192,256 (GRCm38)	T44I	probably damaging	Het
Med13l	A	G	5: 118,755,658 (GRCm38)	T2010A	possibly damaging	Het
Med23	C	T	10: 24,902,181 (GRCm38)	T803M	probably damaging	Het
Mfsd13a	T	C	19: 46,369,277 (GRCm38)	F290S	probably damaging	Het
Myh13	C	T	11: 67,354,927 (GRCm38)	Q1095*	probably null	Het
Nktr	C	A	9: 121,754,326 (GRCm38)	Y93*	probably null	Het
Nox3	A	G	17: 3,685,923 (GRCm38)	S143P	probably damaging	Het
Ntrk2	A	T	13: 58,859,215 (GRCm38)	E210D	probably damaging	Het
Nup210	G	T	6: 91,030,130 (GRCm38)	A568E	probably damaging	Het
Or10ak9	T	A	4: 118,869,138 (GRCm38)	M119K	probably damaging	Het
Or2y1g	A	G	11: 49,280,807 (GRCm38)	I220V	probably benign	Het
Or4g16	A	G	2: 111,306,273 (GRCm38)	T23A	probably benign	Het
Or5as1	T	A	2: 87,149,767 (GRCm38)	K298I	probably damaging	Het
Pdlim5	T	C	3: 142,304,315 (GRCm38)	I289V	probably damaging	Het
Peg10	GC	GCTCC	6: 4,756,452 (GRCm38)		probably benign	Het
Per1	C	T	11: 69,103,257 (GRCm38)	T443M	probably damaging	Het
Plxna1	A	G	6: 89,320,974 (GRCm38)	V1774A	probably damaging	Het
Poteg	A	G	8: 27,450,298 (GRCm38)	Y165C	probably damaging	Het
Prlr	A	G	15: 10,329,184 (GRCm38)	T582A	probably benign	Het
Psma5	A	G	3: 108,265,148 (GRCm38)	E60G	probably damaging	Het
Rsrc1	C	T	3: 66,994,649 (GRCm38)	P44L	unknown	Het
Ryr2	T	C	13: 11,827,559 (GRCm38)	N484S	possibly damaging	Het
Sec31a	A	G	5: 100,393,264 (GRCm38)	I328T	possibly damaging	Het
Slc12a2	G	T	18: 57,919,469 (GRCm38)	V787L	probably benign	Het
St14	C	T	9: 31,106,785 (GRCm38)	R177Q	probably benign	Het
Tcof1	G	C	18: 60,829,051 (GRCm38)	A702G	possibly damaging	Het
Tom1l1	G	T	11: 90,644,161 (GRCm38)		probably null	Het
Ttf1	A	G	2: 29,064,851 (GRCm38)	R76G	probably benign	Het
Ube4a	C	T	9: 44,942,758 (GRCm38)	E581K	probably damaging	Het
Vmn2r114	A	G	17: 23,291,130 (GRCm38)	V792A	probably damaging	Het
Wdr11	T	C	7: 129,607,095 (GRCm38)	I430T	probably benign	Het
Xkr4	T	C	1: 3,671,321 (GRCm38)	K10E	possibly damaging	Het
Zfp451	T	C	1: 33,803,456 (GRCm38)		probably benign	Het

Other mutations in Depdc5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00861:Depdc5	APN	5	32,967,814 (GRCm38)	splice site	probably null
IGL01019:Depdc5	APN	5	32,893,401 (GRCm38)	missense	probably damaging	0.96
IGL01067:Depdc5	APN	5	32,899,067 (GRCm38)	splice site	probably null
IGL01405:Depdc5	APN	5	32,937,689 (GRCm38)	missense	possibly damaging	0.90
IGL01577:Depdc5	APN	5	32,955,897 (GRCm38)	missense	possibly damaging	0.49
IGL01633:Depdc5	APN	5	32,924,200 (GRCm38)	missense	probably damaging	1.00
IGL01998:Depdc5	APN	5	32,945,151 (GRCm38)	splice site	probably benign
IGL02025:Depdc5	APN	5	32,946,632 (GRCm38)	critical splice acceptor site	probably null
IGL02167:Depdc5	APN	5	32,903,801 (GRCm38)	missense	probably damaging	1.00
IGL02537:Depdc5	APN	5	32,967,787 (GRCm38)	missense	probably damaging	1.00
IGL02812:Depdc5	APN	5	32,893,368 (GRCm38)	splice site	probably benign
IGL03001:Depdc5	APN	5	32,945,090 (GRCm38)	missense	possibly damaging	0.74
IGL03253:Depdc5	APN	5	32,868,813 (GRCm38)	unclassified	probably benign
alligator	UTSW	5	32,964,507 (GRCm38)	splice site	probably null
lagarto	UTSW	5	32,979,508 (GRCm38)	missense	probably damaging	1.00
sauros	UTSW	5	32,986,966 (GRCm38)	missense	possibly damaging	0.92
IGL02988:Depdc5	UTSW	5	32,956,167 (GRCm38)	splice site	probably null
R0038:Depdc5	UTSW	5	32,868,853 (GRCm38)	missense	probably benign	0.01
R0038:Depdc5	UTSW	5	32,868,853 (GRCm38)	missense	probably benign	0.01
R0153:Depdc5	UTSW	5	32,933,937 (GRCm38)	splice site	probably benign
R0179:Depdc5	UTSW	5	32,901,574 (GRCm38)	unclassified	probably benign
R0212:Depdc5	UTSW	5	32,912,242 (GRCm38)	missense	probably benign	0.00
R0239:Depdc5	UTSW	5	32,943,240 (GRCm38)	missense	probably damaging	1.00
R0239:Depdc5	UTSW	5	32,943,240 (GRCm38)	missense	probably damaging	1.00
R0302:Depdc5	UTSW	5	32,904,546 (GRCm38)	critical splice donor site	probably benign
R0511:Depdc5	UTSW	5	32,945,028 (GRCm38)	nonsense	probably null
R0677:Depdc5	UTSW	5	32,901,470 (GRCm38)	missense	probably damaging	1.00
R0884:Depdc5	UTSW	5	32,917,978 (GRCm38)	missense	possibly damaging	0.94
R0973:Depdc5	UTSW	5	32,986,966 (GRCm38)	missense	possibly damaging	0.92
R1314:Depdc5	UTSW	5	32,877,074 (GRCm38)	missense	probably damaging	1.00
R1611:Depdc5	UTSW	5	32,990,953 (GRCm38)	missense	probably damaging	1.00
R1687:Depdc5	UTSW	5	32,910,407 (GRCm38)	critical splice acceptor site	probably benign
R1748:Depdc5	UTSW	5	32,917,942 (GRCm38)	missense	probably benign	0.24
R1903:Depdc5	UTSW	5	32,910,407 (GRCm38)	critical splice acceptor site	probably benign
R1956:Depdc5	UTSW	5	32,903,831 (GRCm38)	missense	probably damaging	1.00
R1997:Depdc5	UTSW	5	32,901,906 (GRCm38)	critical splice donor site	probably null
R2079:Depdc5	UTSW	5	32,946,674 (GRCm38)	missense	possibly damaging	0.75
R2131:Depdc5	UTSW	5	32,990,781 (GRCm38)	nonsense	probably null
R2291:Depdc5	UTSW	5	32,979,402 (GRCm38)	missense	probably damaging	1.00
R2422:Depdc5	UTSW	5	32,991,035 (GRCm38)	missense	probably damaging	1.00
R2851:Depdc5	UTSW	5	32,924,171 (GRCm38)	missense	probably damaging	0.96
R2852:Depdc5	UTSW	5	32,924,171 (GRCm38)	missense	probably damaging	0.96
R2937:Depdc5	UTSW	5	32,901,621 (GRCm38)	splice site	probably null
R2938:Depdc5	UTSW	5	32,901,621 (GRCm38)	splice site	probably null
R2974:Depdc5	UTSW	5	32,934,017 (GRCm38)	critical splice donor site	probably null
R3884:Depdc5	UTSW	5	32,944,077 (GRCm38)	missense	probably damaging	1.00
R3967:Depdc5	UTSW	5	32,944,115 (GRCm38)	nonsense	probably null
R4118:Depdc5	UTSW	5	32,964,635 (GRCm38)	missense	probably damaging	1.00
R4197:Depdc5	UTSW	5	32,991,203 (GRCm38)	missense	possibly damaging	0.93
R4407:Depdc5	UTSW	5	32,904,534 (GRCm38)	critical splice donor site	probably null
R4534:Depdc5	UTSW	5	32,910,407 (GRCm38)	critical splice acceptor site	probably benign
R4535:Depdc5	UTSW	5	32,910,407 (GRCm38)	critical splice acceptor site	probably benign
R4538:Depdc5	UTSW	5	32,983,946 (GRCm38)	missense	probably damaging	1.00
R4613:Depdc5	UTSW	5	32,975,446 (GRCm38)	missense	probably damaging	1.00
R4736:Depdc5	UTSW	5	32,975,322 (GRCm38)	missense	probably benign
R4738:Depdc5	UTSW	5	32,975,322 (GRCm38)	missense	probably benign
R4765:Depdc5	UTSW	5	32,937,635 (GRCm38)	missense	probably damaging	1.00
R5021:Depdc5	UTSW	5	32,979,414 (GRCm38)	missense	probably damaging	1.00
R5259:Depdc5	UTSW	5	32,938,291 (GRCm38)	missense	probably damaging	1.00
R5261:Depdc5	UTSW	5	32,938,291 (GRCm38)	missense	probably damaging	1.00
R5541:Depdc5	UTSW	5	32,864,629 (GRCm38)	utr 5 prime	probably benign
R5594:Depdc5	UTSW	5	32,901,490 (GRCm38)	missense	possibly damaging	0.46
R5929:Depdc5	UTSW	5	32,975,506 (GRCm38)	nonsense	probably null
R6132:Depdc5	UTSW	5	32,910,467 (GRCm38)	missense	probably damaging	0.99
R6146:Depdc5	UTSW	5	32,968,731 (GRCm38)	missense	probably benign	0.01
R6336:Depdc5	UTSW	5	32,964,507 (GRCm38)	splice site	probably null
R6468:Depdc5	UTSW	5	32,912,231 (GRCm38)	missense	probably benign	0.02
R6969:Depdc5	UTSW	5	32,983,860 (GRCm38)	missense	probably damaging	1.00
R7002:Depdc5	UTSW	5	32,877,158 (GRCm38)	splice site	probably null
R7066:Depdc5	UTSW	5	32,901,848 (GRCm38)	missense	probably benign	0.08
R7231:Depdc5	UTSW	5	32,901,865 (GRCm38)	missense	possibly damaging	0.92
R7264:Depdc5	UTSW	5	32,967,745 (GRCm38)	missense	probably benign
R7302:Depdc5	UTSW	5	32,979,508 (GRCm38)	missense	probably damaging	1.00
R7386:Depdc5	UTSW	5	32,927,936 (GRCm38)	missense	probably benign
R7564:Depdc5	UTSW	5	32,901,510 (GRCm38)	missense	probably damaging	1.00
R7636:Depdc5	UTSW	5	32,917,983 (GRCm38)	missense	probably benign
R7795:Depdc5	UTSW	5	32,944,103 (GRCm38)	missense	probably damaging	1.00
R7845:Depdc5	UTSW	5	32,903,915 (GRCm38)	splice site	probably null
R8013:Depdc5	UTSW	5	32,973,842 (GRCm38)	missense	probably benign	0.01
R8037:Depdc5	UTSW	5	32,959,348 (GRCm38)	critical splice donor site	probably null
R8038:Depdc5	UTSW	5	32,959,348 (GRCm38)	critical splice donor site	probably null
R8065:Depdc5	UTSW	5	32,895,908 (GRCm38)	missense	possibly damaging	0.89
R8067:Depdc5	UTSW	5	32,895,908 (GRCm38)	missense	possibly damaging	0.89
R8108:Depdc5	UTSW	5	32,945,049 (GRCm38)	missense	probably benign	0.01
R8112:Depdc5	UTSW	5	32,968,706 (GRCm38)	missense	possibly damaging	0.67
R8213:Depdc5	UTSW	5	32,937,637 (GRCm38)	missense	probably damaging	1.00
R8382:Depdc5	UTSW	5	32,927,898 (GRCm38)	missense	probably benign	0.00
R8680:Depdc5	UTSW	5	32,944,038 (GRCm38)	missense	possibly damaging	0.48
R8743:Depdc5	UTSW	5	32,924,243 (GRCm38)	missense	probably benign	0.10
R8754:Depdc5	UTSW	5	32,979,537 (GRCm38)	missense	probably benign	0.00
R9157:Depdc5	UTSW	5	32,945,108 (GRCm38)	missense	probably damaging	0.98
R9364:Depdc5	UTSW	5	32,964,732 (GRCm38)	missense	probably benign
R9441:Depdc5	UTSW	5	32,937,698 (GRCm38)	missense	probably benign	0.03
R9450:Depdc5	UTSW	5	32,934,010 (GRCm38)	missense	probably benign
R9459:Depdc5	UTSW	5	32,990,773 (GRCm38)	missense	probably damaging	0.99
R9554:Depdc5	UTSW	5	32,964,732 (GRCm38)	missense	probably benign
R9569:Depdc5	UTSW	5	32,867,977 (GRCm38)	missense	probably damaging	0.98
R9647:Depdc5	UTSW	5	32,924,223 (GRCm38)	missense	possibly damaging	0.94
R9688:Depdc5	UTSW	5	32,897,932 (GRCm38)	nonsense	probably null
X0027:Depdc5	UTSW	5	32,904,292 (GRCm38)	missense	probably damaging	1.00
Z1176:Depdc5	UTSW	5	32,943,282 (GRCm38)	missense	possibly damaging	0.87

Predicted Primers

PCR Primer
(F):5'- TGGGACAGGTCTTCAGAATACATG -3'
(R):5'- TACCTACAGGAAAAGTGTGCATCC -3'

Sequencing Primer
(F):5'- CCTAGGTTTTTGCTAGCCT -3'
(R):5'- ATCCAGCGCCTTCTGTTGGAG -3'

Posted On

2018-11-06