Mutagenetix > Incidental Mutation

Incidental Mutation 'R5366:Atg4d'

429349

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

042944-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5366 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

21176496-21186133 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 21179948 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Aspartic acid at position 273 (V273D)

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 damaging
Transcript: ENSMUST00000065005
AA Change: V273D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000068450
Gene: ENSMUSG00000002820
AA Change: V273D

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: ENSMUST00000215767

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000216826

Predicted Effect

probably benign
Transcript: ENSMUST00000217269

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000217591

Meta Mutation Damage Score

0.9602

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.2%

Validation Efficiency

100% (77/77)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb5	T	C	12: 118,831,665 (GRCm39)	N1229S	possibly damaging	Het
Adgre1	G	A	17: 57,709,817 (GRCm39)	C158Y	probably benign	Het
Ahnak	T	A	19: 8,994,099 (GRCm39)	S5128T	possibly damaging	Het
Ankrd36	T	A	11: 5,542,841 (GRCm39)	C322*	probably null	Het
Ano1	T	A	7: 144,207,946 (GRCm39)	T113S	possibly damaging	Het
Apeh	A	T	9: 107,969,005 (GRCm39)	S321T	probably benign	Het
Cacna2d4	A	G	6: 119,251,279 (GRCm39)	D489G	probably damaging	Het
Cd47	T	C	16: 49,716,736 (GRCm39)	F256L	probably damaging	Het
Cd84	A	T	1: 171,700,872 (GRCm39)	D211V	probably damaging	Het
Cfap46	A	G	7: 139,230,802 (GRCm39)	L942P	probably damaging	Het
Cfh	A	C	1: 140,063,973 (GRCm39)	C434W	probably damaging	Het
Chst2	T	C	9: 95,287,518 (GRCm39)	D276G	probably damaging	Het
Ctsq	T	C	13: 61,184,913 (GRCm39)	T258A	probably benign	Het
Degs1	C	A	1: 182,106,927 (GRCm39)	D111Y	probably benign	Het
Dhps	T	A	8: 85,801,413 (GRCm39)	D313E	probably damaging	Het
Dipk1c	T	A	18: 84,748,720 (GRCm39)	L106Q	probably damaging	Het
Dock9	A	G	14: 121,815,615 (GRCm39)	C1645R	probably damaging	Het
Efcab7	A	C	4: 99,761,931 (GRCm39)	D407A	possibly damaging	Het
Eif3a	G	T	19: 60,767,971 (GRCm39)	T189N	probably benign	Het
Ep300	T	A	15: 81,500,301 (GRCm39)	L57M	probably benign	Het
Exoc6b	T	A	6: 84,867,513 (GRCm39)	I300L	probably benign	Het
Fzd8	T	C	18: 9,213,880 (GRCm39)	S321P	probably damaging	Het
Garre1	A	T	7: 33,941,713 (GRCm39)	M657K	possibly damaging	Het
Gm9920	T	A	15: 54,975,705 (GRCm39)		probably benign	Het
Gucy2c	A	G	6: 136,697,739 (GRCm39)	I668T	probably damaging	Het
Irgc	C	T	7: 24,132,851 (GRCm39)		probably benign	Het
Jsrp1	G	T	10: 80,646,030 (GRCm39)	S143*	probably null	Het
Kctd4	T	C	14: 76,200,259 (GRCm39)	Y77H	probably damaging	Het
Klhdc1	T	A	12: 69,329,924 (GRCm39)	I351N	probably damaging	Het
Klra17	C	T	6: 129,851,858 (GRCm39)	E5K	possibly damaging	Het
Mapk8	A	T	14: 33,112,686 (GRCm39)	V211E	probably damaging	Het
Mdn1	C	T	4: 32,723,690 (GRCm39)	P2542L	probably damaging	Het
Mrc1	T	C	2: 14,326,725 (GRCm39)	Y1208H	probably benign	Het
Mrps16	A	T	14: 20,441,523 (GRCm39)	S94T	probably benign	Het
Muc5ac	A	G	7: 141,361,287 (GRCm39)	T1533A	probably benign	Het
Myh10	A	T	11: 68,651,518 (GRCm39)	D287V	probably damaging	Het
Obscn	T	C	11: 58,971,086 (GRCm39)	T2476A	probably damaging	Het
Olfm2	T	A	9: 20,579,708 (GRCm39)	T356S	probably benign	Het
Or4f60	T	C	2: 111,902,823 (GRCm39)	Y35C	possibly damaging	Het
P2rx2	T	A	5: 110,489,694 (GRCm39)	N108I	probably damaging	Het
Pbx4	A	T	8: 70,322,820 (GRCm39)	T309S	probably benign	Het
Phyhip	C	A	14: 70,704,295 (GRCm39)	H171Q	probably benign	Het
Pou4f3	A	G	18: 42,528,819 (GRCm39)	E254G	probably damaging	Het
Pxdn	C	A	12: 30,052,899 (GRCm39)	H845Q	probably damaging	Het
Rgcc	T	C	14: 79,529,123 (GRCm39)	T111A	probably benign	Het
Rptor	G	A	11: 119,734,539 (GRCm39)	G514D	probably damaging	Het
Scara5	CG	C	14: 65,997,111 (GRCm39)		probably null	Het
Sgsm1	C	A	5: 113,398,905 (GRCm39)	E722D	possibly damaging	Het
Soat1	A	T	1: 156,272,181 (GRCm39)	D101E	probably benign	Het
Spag5	T	A	11: 78,211,152 (GRCm39)		probably null	Het
Spata31	A	T	13: 65,068,273 (GRCm39)	E140D	probably damaging	Het
Srrm2	T	A	17: 24,037,678 (GRCm39)	S1537T	probably benign	Het
Stam2	G	A	2: 52,626,305 (GRCm39)		probably benign	Het
Tbc1d4	G	T	14: 101,845,412 (GRCm39)	T162K	possibly damaging	Het
Tmem163	A	C	1: 127,428,042 (GRCm39)		probably benign	Het
Tmem43	T	C	6: 91,455,240 (GRCm39)	V72A	probably benign	Het
Tmprss11c	G	A	5: 86,429,993 (GRCm39)	T24I	possibly damaging	Het
Trerf1	A	T	17: 47,626,116 (GRCm39)		noncoding transcript	Het
Trim44	A	G	2: 102,230,476 (GRCm39)	L185P	probably damaging	Het
Tspyl1	A	G	10: 34,158,341 (GRCm39)	D22G	possibly damaging	Het
Ttn	A	T	2: 76,641,587 (GRCm39)	L5176Q	possibly damaging	Het
Tyro3	G	A	2: 119,635,312 (GRCm39)	R201Q	probably damaging	Het
Ubxn2a	T	A	12: 4,930,741 (GRCm39)	K206N	probably benign	Het
Usp17lb	G	T	7: 104,489,615 (GRCm39)	H436Q	possibly damaging	Het
Vps9d1	A	G	8: 123,971,853 (GRCm39)	I584T	possibly damaging	Het
Vrk1	T	A	12: 106,022,078 (GRCm39)	M131K	possibly damaging	Het
Wdr87-ps	A	C	7: 29,232,964 (GRCm39)		noncoding transcript	Het
Zfp827	A	T	8: 79,912,333 (GRCm39)	K986N	possibly damaging	Het
Zswim4	A	G	8: 84,939,419 (GRCm39)	M821T	probably benign	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
R2497:Atg4d	UTSW	9	21,184,682 (GRCm39)	nonsense	probably null
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'- TCGGTCTACATCGGCTAGTG -3'
(R):5'- TTGGTACAGGATTCCCACACC -3'

Sequencing Primer
(F):5'- CTAGTGGAGCTTGGGCGGAG -3'
(R):5'- AAATCGGGGCTTTGGGTA -3'

Posted On

2016-09-06