Mutagenetix > Incidental Mutation

Incidental Mutation 'R9450:Depdc5'

714185

Institutional Source

Beutler Lab

Gene Symbol

Depdc5

Ensembl Gene

ENSMUSG00000037426

Gene Name

DEP domain containing 5

Synonyms

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9450 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

32863701-32994236 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 32934010 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 721 (D721G)

Ref Sequence

ENSEMBL: ENSMUSP00000113862 (fasta)

Gene Model

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

AlphaFold

P61460

Predicted Effect

probably benign
Transcript: ENSMUST00000049780
AA Change: D721G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000052807
Gene: ENSMUSG00000037426
AA Change: D721G

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

probably benign
Transcript: ENSMUST00000087897
AA Change: D721G

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000085207
Gene: ENSMUSG00000037426
AA Change: D721G

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 benign
Transcript: ENSMUST00000119705
AA Change: D721G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000113862
Gene: ENSMUSG00000037426
AA Change: D721G

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 benign
Transcript: ENSMUST00000120902
AA Change: D721G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000113980
Gene: ENSMUSG00000037426
AA Change: D721G

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
AA Change: D74G

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000120120
Gene: ENSMUSG00000037426
AA Change: D74G

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

SMART Domains

Protein: ENSMUSP00000121089
Gene: ENSMUSG00000037426
AA Change: D118G

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2200002D01Rik	CCTTCTCCTTCTTCTCCTTCTTCTCCTTCTTCTCCATCTTCTCCTTCTTC	CCTTCTCCTTCTTCTCCTTCTTCTCCATCTTCTCCTTCTTC	7: 29,247,623 (GRCm38)		probably benign	Het
2810004N23Rik	T	C	8: 124,840,476 (GRCm38)	K229E	probably damaging	Het
9030624J02Rik	T	C	7: 118,752,895 (GRCm38)		probably null	Het
Abca8b	T	C	11: 109,969,104 (GRCm38)	T523A	probably damaging	Het
Adamts18	G	T	8: 113,764,310 (GRCm38)	D508E	probably benign	Het
Arap2	T	C	5: 62,698,419 (GRCm38)	E558G	probably benign	Het
Arid4a	A	T	12: 71,072,600 (GRCm38)	D331V		Het
Ash1l	A	T	3: 89,007,832 (GRCm38)	K1923M	possibly damaging	Het
Atad2b	T	A	12: 5,013,859 (GRCm38)	S947T	probably benign	Het
B4galt1	A	T	4: 40,853,804 (GRCm38)	M1K	probably null	Het
Ccpg1	G	A	9: 72,997,421 (GRCm38)	S4N	unknown	Het
Cfap43	A	T	19: 47,897,871 (GRCm38)	L102M	probably benign	Het
Clic6	T	C	16: 92,530,756 (GRCm38)	I483T	possibly damaging	Het
Col6a6	A	T	9: 105,784,174 (GRCm38)	D245E	probably benign	Het
Cpsf7	G	A	19: 10,540,849 (GRCm38)		probably null	Het
Dhx29	C	T	13: 112,947,328 (GRCm38)	T639I	possibly damaging	Het
Dock7	T	C	4: 98,973,189 (GRCm38)	E1397G	unknown	Het
Dsp	C	T	13: 38,192,403 (GRCm38)	T1388M	probably damaging	Het
Fam186b	C	T	15: 99,285,544 (GRCm38)	G73D	probably damaging	Het
Ganab	A	G	19: 8,915,712 (GRCm38)	D960G	probably damaging	Het
Gria1	T	C	11: 57,309,789 (GRCm38)	V764A	probably damaging	Het
Grk3	T	C	5: 112,915,047 (GRCm38)	K645E	probably benign	Het
Hecw2	A	T	1: 53,839,029 (GRCm38)	Y1339*	probably null	Het
Hmcn2	C	A	2: 31,426,833 (GRCm38)	T3808N	probably damaging	Het
Il20rb	A	T	9: 100,473,002 (GRCm38)	N129K	possibly damaging	Het
Iqca1l	T	A	5: 24,549,449 (GRCm38)	I395F	probably benign	Het
Itgb4	T	C	11: 115,983,271 (GRCm38)	Y340H	probably damaging	Het
Itgb6	T	C	2: 60,628,028 (GRCm38)	I460M	probably benign	Het
Kat14	T	C	2: 144,400,819 (GRCm38)	I599T	possibly damaging	Het
Kif1b	A	C	4: 149,238,010 (GRCm38)	D817E	probably benign	Het
Lamb2	T	A	9: 108,480,561 (GRCm38)	C94*	probably null	Het
Larp1	T	C	11: 58,051,064 (GRCm38)	S743P	probably damaging	Het
Ldlrap1	T	C	4: 134,747,179 (GRCm38)	N267S	probably damaging	Het
Ltbp2	G	A	12: 84,791,090 (GRCm38)	P1192L	probably benign	Het
Ltf	T	C	9: 111,021,996 (GRCm38)	L92P	probably damaging	Het
Ly6g2	T	A	15: 75,220,725 (GRCm38)	C98S	probably damaging	Het
Mns1	C	A	9: 72,452,608 (GRCm38)	Q347K	probably benign	Het
Myof	A	T	19: 37,960,926 (GRCm38)	F611I	probably damaging	Het
Nop56	T	C	2: 130,275,681 (GRCm38)	L76P	probably damaging	Het
Nphp1	T	C	2: 127,774,088 (GRCm38)	H114R		Het
Or10g3	G	C	14: 52,372,653 (GRCm38)	Y133*	probably null	Het
Or1e30	C	A	11: 73,787,275 (GRCm38)	N112K	possibly damaging	Het
Or4k36	T	A	2: 111,316,053 (GRCm38)	N191K	probably benign	Het
Pcdha12	A	G	18: 37,020,939 (GRCm38)	D237G	probably damaging	Het
Pierce1	TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC	TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC	2: 28,466,110 (GRCm38)		probably benign	Het
Pitpnm3	A	T	11: 72,061,586 (GRCm38)	M593K	possibly damaging	Het
Plxdc1	C	T	11: 97,954,855 (GRCm38)	V211I	probably damaging	Het
Prkn	C	A	17: 11,838,634 (GRCm38)	H301N	possibly damaging	Het
Prpf38a	A	T	4: 108,572,875 (GRCm38)	H143Q	probably damaging	Het
Sdk2	T	C	11: 113,806,279 (GRCm38)	T1769A	probably benign	Het
Spata31f1e	G	T	4: 42,793,833 (GRCm38)	Q100K	probably benign	Het
Stab1	T	C	14: 31,162,939 (GRCm38)	D153G	possibly damaging	Het
Tm7sf3	C	T	6: 146,623,681 (GRCm38)	D89N	possibly damaging	Het
Tnrc6b	T	A	15: 80,880,436 (GRCm38)	M713K	probably benign	Het
Top2a	T	C	11: 99,003,608 (GRCm38)	K966E	possibly damaging	Het
Vars2	T	C	17: 35,662,135 (GRCm38)	T421A	probably damaging	Het
Vmn1r1	A	T	1: 182,157,205 (GRCm38)	C298*	probably null	Het
Vwa3a	T	C	7: 120,804,030 (GRCm38)		probably null	Het
Vwa5b1	G	T	4: 138,588,629 (GRCm38)	Q601K	possibly damaging	Het
Zbtb46	T	C	2: 181,395,488 (GRCm38)	K454E	probably damaging	Het
Zfp426	T	C	9: 20,470,281 (GRCm38)	H470R	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
R6911:Depdc5	UTSW	5	32,924,192 (GRCm38)	missense	probably damaging	1.00
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
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'- TACCCATTTCATAATTGGCACTTGG -3'
(R):5'- GCCGTGTGTCCTGAATTACAC -3'

Sequencing Primer
(F):5'- ATTTCATAATTGGCACTTGGTTTGTG -3'
(R):5'- GTGTCCTGAATTACACATCCTGGAG -3'

Posted On

2022-06-15