Incidental Mutation 'R1724:Atg4d'
ID 191682
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 039756-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1724 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 21176496-21186133 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 21179741 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Tyrosine at position 230 (H230Y)
Ref Sequence ENSEMBL: ENSMUSP00000068450 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000065005]
AlphaFold Q8BGV9
Predicted Effect probably damaging
Transcript: ENSMUST00000065005
AA Change: H230Y

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000068450
Gene: ENSMUSG00000002820
AA Change: H230Y

DomainStartEndE-ValueType
low complexity region 39 53 N/A INTRINSIC
Pfam:Peptidase_C54 109 411 5.7e-107 PFAM
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 0.9411 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.4%
  • 20x: 93.0%
Validation Efficiency 98% (50/51)
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: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts13 T C 2: 26,881,306 (GRCm39) V761A probably benign Het
Arap1 G T 7: 101,049,733 (GRCm39) A1032S possibly damaging Het
Auh G A 13: 52,989,532 (GRCm39) P308L probably benign Het
Bcdin3d T A 15: 99,368,561 (GRCm39) K213* probably null Het
Cep295nl T A 11: 118,223,854 (GRCm39) E330V probably benign Het
Col10a1 A G 10: 34,271,714 (GRCm39) Y562C probably damaging Het
Col9a2 G A 4: 120,911,099 (GRCm39) R578Q probably damaging Het
Creld1 A G 6: 113,461,535 (GRCm39) D85G possibly damaging Het
Cth A T 3: 157,619,364 (GRCm39) V153D probably damaging Het
Dazap2 T A 15: 100,515,884 (GRCm39) Y71N probably damaging Het
Ddah1 A C 3: 145,597,261 (GRCm39) D269A probably damaging Het
Dhx9 A C 1: 153,334,234 (GRCm39) D975E probably benign Het
Erich3 T A 3: 154,467,964 (GRCm39) D805E possibly damaging Het
Fam83f T G 15: 80,576,468 (GRCm39) V373G possibly damaging Het
Gabpb2 T C 3: 95,113,826 (GRCm39) D19G probably damaging Het
Gabrr1 T A 4: 33,161,651 (GRCm39) M325K probably damaging Het
Galntl5 T G 5: 25,425,120 (GRCm39) N379K possibly damaging Het
Gm10277 TC T 11: 77,676,828 (GRCm39) probably null Het
Gm42791 C A 5: 148,896,311 (GRCm39) probably benign Het
Gm5356 G A 8: 89,913,684 (GRCm39) noncoding transcript Het
Kifap3 C T 1: 163,610,666 (GRCm39) R49* probably null Het
Kmt2c C T 5: 25,520,003 (GRCm39) G2036R probably damaging Het
Lce1l A T 3: 92,757,726 (GRCm39) V44E unknown Het
Lmbr1 T A 5: 29,566,081 (GRCm39) E48D probably benign Het
Nes C A 3: 87,884,748 (GRCm39) N958K probably benign Het
Nwd1 A C 8: 73,438,248 (GRCm39) H1432P probably damaging Het
Or2d2b G A 7: 106,705,409 (GRCm39) H220Y probably benign Het
Or52h9 T C 7: 104,202,435 (GRCm39) F103S probably damaging Het
Osgepl1 A G 1: 53,357,062 (GRCm39) T75A probably benign Het
Perm1 T C 4: 156,302,529 (GRCm39) S358P possibly damaging Het
Pramel14 C T 4: 143,720,002 (GRCm39) G121D probably benign Het
Ptk2 A G 15: 73,114,255 (GRCm39) V701A possibly damaging Het
Sdc4 G T 2: 164,273,206 (GRCm39) Q35K probably benign Het
Secisbp2 A G 13: 51,824,882 (GRCm39) S377G probably benign Het
Spag16 G C 1: 70,532,941 (GRCm39) G540A probably damaging Het
Sun1 T A 5: 139,221,480 (GRCm39) D517E probably benign Het
Taf3 A G 2: 9,957,177 (GRCm39) V177A probably benign Het
Thbs2 A G 17: 14,906,162 (GRCm39) L246P possibly damaging Het
Tle7 C A 8: 110,836,795 (GRCm39) T227N probably damaging Het
Trpm1 G T 7: 63,885,569 (GRCm39) G862* probably null Het
Trpm8 A T 1: 88,278,578 (GRCm39) T584S possibly damaging Het
Ythdc2 T C 18: 44,961,757 (GRCm39) S2P probably benign Het
Zc2hc1c G T 12: 85,336,586 (GRCm39) R81L probably benign Het
Zfp292 C A 4: 34,811,237 (GRCm39) L602F probably damaging Het
Other mutations in Atg4d
AlleleSourceChrCoordTypePredicted EffectPPH 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
R1912:Atg4d UTSW 9 21,183,935 (GRCm39) missense probably damaging 1.00
R2497:Atg4d UTSW 9 21,184,682 (GRCm39) nonsense probably null
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'- GTGCCACAGTTTAGCTCTCAGTGTC -3'
(R):5'- GCTGACTTCTGAGCAACTCTCCAC -3'

Sequencing Primer
(F):5'- TCTCGTCCTCAGACTGGAG -3'
(R):5'- GAGCAACTCTCCACAGCTTTC -3'
Posted On 2014-05-14