Mutagenetix > Incidental Mutation

Incidental Mutation 'R2497:Atg4d'

251069

Institutional Source

Beutler Lab

Gene Symbol

Atg4d

Ensembl Gene

ENSMUSG00000002820

Gene Name

autophagy related 4D, cysteine peptidase

Synonyms

Apg4d, 9830134P12Rik, APG4-D, Autl4

MMRRC Submission

040411-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2497 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

21176496-21186133 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

C to T at 21184682 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Stop codon at position 459 (R459*)

Ref Sequence

ENSEMBL: ENSMUSP00000068450 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038671] [ENSMUST00000065005] [ENSMUST00000184326]

AlphaFold

Q8BGV9

Predicted Effect

probably benign
Transcript: ENSMUST00000038671

SMART Domains

Protein: ENSMUSP00000039688
Gene: ENSMUSG00000035047

Domain	Start	End	E-Value	Type
low complexity region	20	34	N/A	INTRINSIC
low complexity region	50	60	N/A	INTRINSIC
low complexity region	98	112	N/A	INTRINSIC
low complexity region	181	195	N/A	INTRINSIC
Pfam:Kri1	346	439	3.2e-27	PFAM
Pfam:Kri1_C	507	595	8.4e-37	PFAM
low complexity region	653	666	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000065005
AA Change: R459*

SMART Domains

Protein: ENSMUSP00000068450
Gene: ENSMUSG00000002820
AA Change: R459*

Domain	Start	End	E-Value	Type
low complexity region	39	53	N/A	INTRINSIC
Pfam:Peptidase_C54	109	411	5.7e-107	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000184326

SMART Domains

Protein: ENSMUSP00000139184
Gene: ENSMUSG00000035047

Domain	Start	End	E-Value	Type
low complexity region	57	71	N/A	INTRINSIC
Pfam:Kri1	207	317	4.4e-27	PFAM
Pfam:Kri1_C	381	472	3.6e-36	PFAM
low complexity region	529	542	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184410

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000192279

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000216826

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000217591

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.1%
20x: 94.3%

Validation Efficiency

100% (60/60)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly. Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation, metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some malignant tumors, and a role for autophagy in controlling the unregulated cell growth linked to cancer has been proposed. This gene belongs to the autophagy-related protein 4 (Atg4) family of C54 endopeptidases. Members of this family encode proteins that play a role in the biogenesis of autophagosomes, which sequester the cytosol and organelles for degradation by lysosomes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

Allele List at MGI

Other mutations in this stock

Total: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acox2	A	G	14: 8,251,612 (GRCm38)	V295A	probably benign	Het
Agrn	T	C	4: 156,258,268 (GRCm39)	E959G	probably benign	Het
Aqp5	T	C	15: 99,489,180 (GRCm39)	F10L	possibly damaging	Het
Arhgap39	C	A	15: 76,609,585 (GRCm39)	V1025L	probably damaging	Het
Atp11b	A	G	3: 35,909,294 (GRCm39)	S1163G	probably damaging	Het
Atp13a5	G	T	16: 29,157,889 (GRCm39)	S173*	probably null	Het
Atp6v1g2	T	A	17: 35,455,762 (GRCm39)	I8N	probably damaging	Het
Ccdc77	C	T	6: 120,302,433 (GRCm39)	G430R	possibly damaging	Het
Cdc34b	A	G	11: 94,633,207 (GRCm39)	T136A	probably benign	Het
Cdkal1	A	G	13: 29,658,524 (GRCm39)	S23P	unknown	Het
Cdkl2	T	A	5: 92,156,857 (GRCm39)	H566L	probably benign	Het
Cers6	T	C	2: 68,901,790 (GRCm39)		probably benign	Het
Cfap251	T	C	5: 123,421,432 (GRCm39)	V98A	probably damaging	Het
Clspn	A	G	4: 126,466,140 (GRCm39)	T557A	possibly damaging	Het
Cmya5	T	C	13: 93,234,513 (GRCm39)	T192A	possibly damaging	Het
Csmd3	CCTTTGCGCTT	CCTT	15: 47,604,632 (GRCm39)		probably null	Het
Dnah17	T	G	11: 117,977,850 (GRCm39)		probably null	Het
Dnah8	C	T	17: 30,960,339 (GRCm39)	Q2239*	probably null	Het
Dscaml1	T	C	9: 45,656,376 (GRCm39)	V1572A	probably benign	Het
Elfn2	C	G	15: 78,558,464 (GRCm39)	E28Q	probably damaging	Het
Enam	T	A	5: 88,650,553 (GRCm39)	N687K	probably benign	Het
Flywch1	G	A	17: 23,974,685 (GRCm39)	R652W	probably benign	Het
Gm5612	T	C	9: 18,338,975 (GRCm39)		probably benign	Het
Hgsnat	C	T	8: 26,435,280 (GRCm39)	W618*	probably null	Het
Mmp3	A	G	9: 7,450,131 (GRCm39)	T288A	probably benign	Het
Mtmr4	T	A	11: 87,491,649 (GRCm39)	F168L	probably damaging	Het
Mtres1	T	C	10: 43,401,263 (GRCm39)		probably benign	Het
Myo1d	T	A	11: 80,565,647 (GRCm39)	N393Y	probably damaging	Het
Nacc2	A	T	2: 25,979,580 (GRCm39)	Y285*	probably null	Het
Nf1	G	T	11: 79,334,710 (GRCm39)	G844V	probably damaging	Het
Nox4	T	A	7: 86,945,084 (GRCm39)	Y113*	probably null	Het
Pcdha3	T	C	18: 37,080,556 (GRCm39)	C433R	probably benign	Het
Pde6c	A	G	19: 38,142,142 (GRCm39)	I358V	probably damaging	Het
Pdgfrb	A	T	18: 61,211,700 (GRCm39)	D819V	possibly damaging	Het
Phf3	C	A	1: 30,869,095 (GRCm39)	R651L	probably damaging	Het
Prrx1	A	G	1: 163,075,834 (GRCm39)	V244A	possibly damaging	Het
Ptges	C	T	2: 30,782,722 (GRCm39)	G110D	possibly damaging	Het
Rab27a	T	C	9: 72,992,263 (GRCm39)	L97P	probably damaging	Het
Rnf20	G	A	4: 49,652,676 (GRCm39)		probably null	Het
Sdad1	T	C	5: 92,447,958 (GRCm39)	N259S	probably benign	Het
Serpinb9d	T	C	13: 33,380,500 (GRCm39)	S129P	probably damaging	Het
Slc1a4	T	C	11: 20,282,620 (GRCm39)		probably benign	Het
Smyd2	T	A	1: 189,617,534 (GRCm39)	N300I	possibly damaging	Het
Snd1	A	G	6: 28,888,078 (GRCm39)	I875V	probably benign	Het
Ssh1	T	C	5: 114,096,919 (GRCm39)	N174S	probably damaging	Het
Stimate	C	T	14: 30,594,537 (GRCm39)	L217F	probably damaging	Het
Tanc2	T	C	11: 105,564,319 (GRCm39)		probably null	Het
Tectb	C	G	19: 55,169,431 (GRCm39)		probably benign	Het
Tpcn1	C	T	5: 120,677,063 (GRCm39)		probably null	Het
Unc45b	A	T	11: 82,827,269 (GRCm39)	I699F	probably damaging	Het
Uspl1	C	T	5: 149,124,664 (GRCm39)	P27L	probably damaging	Het
Ylpm1	C	G	12: 85,043,535 (GRCm39)	P91R	probably damaging	Het
Zdhhc23	G	A	16: 43,794,278 (GRCm39)	T132M	probably damaging	Het
Zfp148	T	C	16: 33,316,755 (GRCm39)	Y434H	probably damaging	Het
Zhx2	T	C	15: 57,686,551 (GRCm39)	V640A	possibly damaging	Het

Other mutations in Atg4d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00493:Atg4d	APN	9	21,178,217 (GRCm39)	missense	probably damaging	1.00
BB006:Atg4d	UTSW	9	21,178,260 (GRCm39)	missense	probably null	0.82
BB016:Atg4d	UTSW	9	21,178,260 (GRCm39)	missense	probably null	0.82
R1393:Atg4d	UTSW	9	21,182,129 (GRCm39)	missense	probably damaging	1.00
R1455:Atg4d	UTSW	9	21,182,097 (GRCm39)	missense	probably damaging	1.00
R1724:Atg4d	UTSW	9	21,179,741 (GRCm39)	missense	probably damaging	1.00
R1912:Atg4d	UTSW	9	21,183,935 (GRCm39)	missense	probably damaging	1.00
R5366:Atg4d	UTSW	9	21,179,948 (GRCm39)	missense	probably damaging	1.00
R6563:Atg4d	UTSW	9	21,179,756 (GRCm39)	missense	possibly damaging	0.80
R6709:Atg4d	UTSW	9	21,179,944 (GRCm39)	missense	probably damaging	1.00
R7929:Atg4d	UTSW	9	21,178,260 (GRCm39)	missense	probably null	0.82
R8263:Atg4d	UTSW	9	21,178,335 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CAGCTGTTCAGAGGCTAAGC -3'
(R):5'- CAGATAGGTCTCAGCTGTGTTG -3'

Sequencing Primer
(F):5'- GTCCAGCTGGTCCAGAAAGAC -3'
(R):5'- CTCAGCTGTGTTGGGGAGGAC -3'

Posted On

2014-12-04