Mutagenetix > Incidental Mutation

Incidental Mutation 'R6132:Depdc5'

487172

Institutional Source

Beutler Lab

Gene Symbol

Depdc5

Ensembl Gene

ENSMUSG00000037426

Gene Name

DEP domain containing 5

Synonyms

MMRRC Submission

044279-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6132 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

33021045-33151580 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 33067811 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 410 (S410T)

Ref Sequence

ENSEMBL: ENSMUSP00000113980 (fasta)

Gene Model

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

AlphaFold

P61460

Predicted Effect

probably benign
Transcript: ENSMUST00000049780
AA Change: S410T

PolyPhen 2 Score 0.134 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000052807
Gene: ENSMUSG00000037426
AA Change: S410T

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: S410T

PolyPhen 2 Score 0.647 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000085207
Gene: ENSMUSG00000037426
AA Change: S410T

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: S410T

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

SMART Domains

Protein: ENSMUSP00000113862
Gene: ENSMUSG00000037426
AA Change: S410T

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: S410T

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

SMART Domains

Protein: ENSMUSP00000113980
Gene: ENSMUSG00000037426
AA Change: S410T

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

noncoding transcript
Transcript: ENSMUST00000139098

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000158455

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201802

Predicted Effect

probably benign
Transcript: ENSMUST00000201836

Meta Mutation Damage Score

0.0993

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 94.9%

Validation Efficiency

96% (49/51)

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca15	T	C	7: 119,960,643 (GRCm39)	Y702H	probably benign	Het
Adgrv1	G	T	13: 81,654,195 (GRCm39)	N2225K	probably benign	Het
Afg3l2	G	T	18: 67,554,329 (GRCm39)	L458M	probably damaging	Het
Alkbh5	G	T	11: 60,428,821 (GRCm39)		probably benign	Het
Atp5mc1	A	G	11: 95,965,850 (GRCm39)	M1T	probably null	Het
Crebrf	C	T	17: 26,982,377 (GRCm39)	P588S	probably benign	Het
Ctsr	A	C	13: 61,309,582 (GRCm39)		probably null	Het
Cyp2c68	A	G	19: 39,691,858 (GRCm39)	V355A	possibly damaging	Het
Ddx52	A	G	11: 83,850,283 (GRCm39)	K555E	possibly damaging	Het
Dhx30	A	T	9: 109,914,847 (GRCm39)	I884N	probably damaging	Het
Dlg1	A	T	16: 31,655,059 (GRCm39)	N518I	possibly damaging	Het
Dnah12	T	A	14: 26,439,066 (GRCm39)	I506N	probably damaging	Het
Efcab6	A	G	15: 83,917,173 (GRCm39)	L129P	probably damaging	Het
Erap1	A	G	13: 74,808,401 (GRCm39)	N38D	probably benign	Het
Esf1	A	G	2: 140,001,699 (GRCm39)	F383L	probably benign	Het
Exoc4	A	G	6: 33,735,033 (GRCm39)	E550G	probably damaging	Het
Fbxo44	G	A	4: 148,240,565 (GRCm39)	T221I	probably benign	Het
Gal3st2b	A	T	1: 93,867,688 (GRCm39)	M112L	possibly damaging	Het
Golph3l	C	G	3: 95,499,145 (GRCm39)	P96A	probably benign	Het
Gprc6a	T	A	10: 51,491,356 (GRCm39)	I727F	possibly damaging	Het
Grin3b	T	C	10: 79,812,274 (GRCm39)	L479P	probably damaging	Het
Kdm5a	C	T	6: 120,351,892 (GRCm39)	H161Y	probably damaging	Het
Lman2	A	G	13: 55,510,038 (GRCm39)	S73P	probably benign	Het
Map3k19	T	C	1: 127,778,213 (GRCm39)	N4S	possibly damaging	Het
Mkln1	G	A	6: 31,408,155 (GRCm39)	V161M	probably damaging	Het
Mmel1	C	T	4: 154,979,475 (GRCm39)	H728Y	probably damaging	Het
Nova2	G	A	7: 18,691,794 (GRCm39)	A244T	unknown	Het
Nrcam	T	A	12: 44,617,007 (GRCm39)	Y668N	probably damaging	Het
Oacyl	G	T	18: 65,859,426 (GRCm39)	G255W	probably damaging	Het
Omd	A	C	13: 49,743,843 (GRCm39)	I298L	probably damaging	Het
Or5ac19	A	G	16: 59,089,367 (GRCm39)	V221A	probably damaging	Het
Or5ak24	A	T	2: 85,260,490 (GRCm39)	S228T	probably benign	Het
Or8b36	ATTGCTGTTT	ATTGCTGTTTGCTGTTT	9: 37,937,836 (GRCm39)		probably null	Het
Otor	A	T	2: 142,920,520 (GRCm39)	D34V	probably damaging	Het
Otx1	A	T	11: 21,949,406 (GRCm39)	L24H	probably damaging	Het
Pwwp2a	A	G	11: 43,596,455 (GRCm39)	Y540C	probably damaging	Het
Rttn	T	A	18: 89,133,770 (GRCm39)		probably null	Het
S1pr4	G	A	10: 81,335,030 (GRCm39)	A148V	probably benign	Het
Scn10a	C	T	9: 119,442,761 (GRCm39)	V1495M	possibly damaging	Het
Sel1l3	T	C	5: 53,357,531 (GRCm39)	K154E	possibly damaging	Het
Sema3a	T	G	5: 13,573,142 (GRCm39)		probably null	Het
Slf2	T	A	19: 44,949,300 (GRCm39)	N870K	possibly damaging	Het
Spmip6	C	T	4: 41,517,160 (GRCm39)	M1I	probably null	Het
Syne2	T	C	12: 75,991,921 (GRCm39)	V1962A	probably benign	Het
Tarbp1	T	A	8: 127,161,548 (GRCm39)	I1219F	probably benign	Het
Tet1	A	C	10: 62,649,079 (GRCm39)	C173W	probably damaging	Het
Tnn	A	G	1: 159,973,641 (GRCm39)	F242S	probably damaging	Het
Tollip	A	G	7: 141,443,334 (GRCm39)	S174P	probably benign	Het
Tsr3	G	T	17: 25,460,835 (GRCm39)	D234Y	probably null	Het
Vmn2r106	T	C	17: 20,488,666 (GRCm39)	T578A	probably benign	Het
Zfp457	G	T	13: 67,441,360 (GRCm39)	S309*	probably null	Het

Other mutations in Depdc5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00861:Depdc5	APN	5	33,125,158 (GRCm39)	splice site	probably null
IGL01019:Depdc5	APN	5	33,050,745 (GRCm39)	missense	probably damaging	0.96
IGL01067:Depdc5	APN	5	33,056,411 (GRCm39)	splice site	probably null
IGL01405:Depdc5	APN	5	33,095,033 (GRCm39)	missense	possibly damaging	0.90
IGL01577:Depdc5	APN	5	33,113,241 (GRCm39)	missense	possibly damaging	0.49
IGL01633:Depdc5	APN	5	33,081,544 (GRCm39)	missense	probably damaging	1.00
IGL01998:Depdc5	APN	5	33,102,495 (GRCm39)	splice site	probably benign
IGL02025:Depdc5	APN	5	33,103,976 (GRCm39)	critical splice acceptor site	probably null
IGL02167:Depdc5	APN	5	33,061,145 (GRCm39)	missense	probably damaging	1.00
IGL02537:Depdc5	APN	5	33,125,131 (GRCm39)	missense	probably damaging	1.00
IGL02812:Depdc5	APN	5	33,050,712 (GRCm39)	splice site	probably benign
IGL03001:Depdc5	APN	5	33,102,434 (GRCm39)	missense	possibly damaging	0.74
IGL03253:Depdc5	APN	5	33,026,157 (GRCm39)	unclassified	probably benign
alligator	UTSW	5	33,121,851 (GRCm39)	splice site	probably null
lagarto	UTSW	5	33,136,852 (GRCm39)	missense	probably damaging	1.00
sauros	UTSW	5	33,144,310 (GRCm39)	missense	possibly damaging	0.92
IGL02988:Depdc5	UTSW	5	33,113,511 (GRCm39)	splice site	probably null
R0038:Depdc5	UTSW	5	33,026,197 (GRCm39)	missense	probably benign	0.01
R0038:Depdc5	UTSW	5	33,026,197 (GRCm39)	missense	probably benign	0.01
R0153:Depdc5	UTSW	5	33,091,281 (GRCm39)	splice site	probably benign
R0179:Depdc5	UTSW	5	33,058,918 (GRCm39)	unclassified	probably benign
R0212:Depdc5	UTSW	5	33,069,586 (GRCm39)	missense	probably benign	0.00
R0239:Depdc5	UTSW	5	33,100,584 (GRCm39)	missense	probably damaging	1.00
R0239:Depdc5	UTSW	5	33,100,584 (GRCm39)	missense	probably damaging	1.00
R0302:Depdc5	UTSW	5	33,061,890 (GRCm39)	critical splice donor site	probably benign
R0511:Depdc5	UTSW	5	33,102,372 (GRCm39)	nonsense	probably null
R0677:Depdc5	UTSW	5	33,058,814 (GRCm39)	missense	probably damaging	1.00
R0884:Depdc5	UTSW	5	33,075,322 (GRCm39)	missense	possibly damaging	0.94
R0973:Depdc5	UTSW	5	33,144,310 (GRCm39)	missense	possibly damaging	0.92
R1314:Depdc5	UTSW	5	33,034,418 (GRCm39)	missense	probably damaging	1.00
R1611:Depdc5	UTSW	5	33,148,297 (GRCm39)	missense	probably damaging	1.00
R1687:Depdc5	UTSW	5	33,067,751 (GRCm39)	critical splice acceptor site	probably benign
R1748:Depdc5	UTSW	5	33,075,286 (GRCm39)	missense	probably benign	0.24
R1903:Depdc5	UTSW	5	33,067,751 (GRCm39)	critical splice acceptor site	probably benign
R1956:Depdc5	UTSW	5	33,061,175 (GRCm39)	missense	probably damaging	1.00
R1997:Depdc5	UTSW	5	33,059,250 (GRCm39)	critical splice donor site	probably null
R2079:Depdc5	UTSW	5	33,104,018 (GRCm39)	missense	possibly damaging	0.75
R2131:Depdc5	UTSW	5	33,148,125 (GRCm39)	nonsense	probably null
R2291:Depdc5	UTSW	5	33,136,746 (GRCm39)	missense	probably damaging	1.00
R2422:Depdc5	UTSW	5	33,148,379 (GRCm39)	missense	probably damaging	1.00
R2851:Depdc5	UTSW	5	33,081,515 (GRCm39)	missense	probably damaging	0.96
R2852:Depdc5	UTSW	5	33,081,515 (GRCm39)	missense	probably damaging	0.96
R2937:Depdc5	UTSW	5	33,058,965 (GRCm39)	splice site	probably null
R2938:Depdc5	UTSW	5	33,058,965 (GRCm39)	splice site	probably null
R2974:Depdc5	UTSW	5	33,091,361 (GRCm39)	critical splice donor site	probably null
R3884:Depdc5	UTSW	5	33,101,421 (GRCm39)	missense	probably damaging	1.00
R3967:Depdc5	UTSW	5	33,101,459 (GRCm39)	nonsense	probably null
R4118:Depdc5	UTSW	5	33,121,979 (GRCm39)	missense	probably damaging	1.00
R4197:Depdc5	UTSW	5	33,148,547 (GRCm39)	missense	possibly damaging	0.93
R4407:Depdc5	UTSW	5	33,061,878 (GRCm39)	critical splice donor site	probably null
R4534:Depdc5	UTSW	5	33,067,751 (GRCm39)	critical splice acceptor site	probably benign
R4535:Depdc5	UTSW	5	33,067,751 (GRCm39)	critical splice acceptor site	probably benign
R4538:Depdc5	UTSW	5	33,141,290 (GRCm39)	missense	probably damaging	1.00
R4613:Depdc5	UTSW	5	33,132,790 (GRCm39)	missense	probably damaging	1.00
R4736:Depdc5	UTSW	5	33,132,666 (GRCm39)	missense	probably benign
R4738:Depdc5	UTSW	5	33,132,666 (GRCm39)	missense	probably benign
R4765:Depdc5	UTSW	5	33,094,979 (GRCm39)	missense	probably damaging	1.00
R5021:Depdc5	UTSW	5	33,136,758 (GRCm39)	missense	probably damaging	1.00
R5259:Depdc5	UTSW	5	33,095,635 (GRCm39)	missense	probably damaging	1.00
R5261:Depdc5	UTSW	5	33,095,635 (GRCm39)	missense	probably damaging	1.00
R5541:Depdc5	UTSW	5	33,021,973 (GRCm39)	utr 5 prime	probably benign
R5594:Depdc5	UTSW	5	33,058,834 (GRCm39)	missense	possibly damaging	0.46
R5929:Depdc5	UTSW	5	33,132,850 (GRCm39)	nonsense	probably null
R6146:Depdc5	UTSW	5	33,126,075 (GRCm39)	missense	probably benign	0.01
R6336:Depdc5	UTSW	5	33,121,851 (GRCm39)	splice site	probably null
R6468:Depdc5	UTSW	5	33,069,575 (GRCm39)	missense	probably benign	0.02
R6911:Depdc5	UTSW	5	33,081,536 (GRCm39)	missense	probably damaging	1.00
R6969:Depdc5	UTSW	5	33,141,204 (GRCm39)	missense	probably damaging	1.00
R7002:Depdc5	UTSW	5	33,034,502 (GRCm39)	splice site	probably null
R7066:Depdc5	UTSW	5	33,059,192 (GRCm39)	missense	probably benign	0.08
R7231:Depdc5	UTSW	5	33,059,209 (GRCm39)	missense	possibly damaging	0.92
R7264:Depdc5	UTSW	5	33,125,089 (GRCm39)	missense	probably benign
R7302:Depdc5	UTSW	5	33,136,852 (GRCm39)	missense	probably damaging	1.00
R7386:Depdc5	UTSW	5	33,085,280 (GRCm39)	missense	probably benign
R7564:Depdc5	UTSW	5	33,058,854 (GRCm39)	missense	probably damaging	1.00
R7636:Depdc5	UTSW	5	33,075,327 (GRCm39)	missense	probably benign
R7795:Depdc5	UTSW	5	33,101,447 (GRCm39)	missense	probably damaging	1.00
R7845:Depdc5	UTSW	5	33,061,259 (GRCm39)	splice site	probably null
R8013:Depdc5	UTSW	5	33,131,186 (GRCm39)	missense	probably benign	0.01
R8037:Depdc5	UTSW	5	33,116,692 (GRCm39)	critical splice donor site	probably null
R8038:Depdc5	UTSW	5	33,116,692 (GRCm39)	critical splice donor site	probably null
R8065:Depdc5	UTSW	5	33,053,252 (GRCm39)	missense	possibly damaging	0.89
R8067:Depdc5	UTSW	5	33,053,252 (GRCm39)	missense	possibly damaging	0.89
R8108:Depdc5	UTSW	5	33,102,393 (GRCm39)	missense	probably benign	0.01
R8112:Depdc5	UTSW	5	33,126,050 (GRCm39)	missense	possibly damaging	0.67
R8213:Depdc5	UTSW	5	33,094,981 (GRCm39)	missense	probably damaging	1.00
R8382:Depdc5	UTSW	5	33,085,242 (GRCm39)	missense	probably benign	0.00
R8680:Depdc5	UTSW	5	33,101,382 (GRCm39)	missense	possibly damaging	0.48
R8743:Depdc5	UTSW	5	33,081,587 (GRCm39)	missense	probably benign	0.10
R8754:Depdc5	UTSW	5	33,136,881 (GRCm39)	missense	probably benign	0.00
R9157:Depdc5	UTSW	5	33,102,452 (GRCm39)	missense	probably damaging	0.98
R9364:Depdc5	UTSW	5	33,122,076 (GRCm39)	missense	probably benign
R9441:Depdc5	UTSW	5	33,095,042 (GRCm39)	missense	probably benign	0.03
R9450:Depdc5	UTSW	5	33,091,354 (GRCm39)	missense	probably benign
R9459:Depdc5	UTSW	5	33,148,117 (GRCm39)	missense	probably damaging	0.99
R9554:Depdc5	UTSW	5	33,122,076 (GRCm39)	missense	probably benign
R9569:Depdc5	UTSW	5	33,025,321 (GRCm39)	missense	probably damaging	0.98
R9647:Depdc5	UTSW	5	33,081,567 (GRCm39)	missense	possibly damaging	0.94
R9688:Depdc5	UTSW	5	33,055,276 (GRCm39)	nonsense	probably null
X0027:Depdc5	UTSW	5	33,061,636 (GRCm39)	missense	probably damaging	1.00
Z1176:Depdc5	UTSW	5	33,100,626 (GRCm39)	missense	possibly damaging	0.87

Predicted Primers

PCR Primer
(F):5'- GCAGTTTGCCTTAAGGTTTAGC -3'
(R):5'- CCCTGTTTATGACCCTAGGC -3'

Sequencing Primer
(F):5'- GGTATACTAGGGGCCAACTTTATCC -3'
(R):5'- CCTAGGCAGGGGAGAGG -3'

Posted On

2017-10-10