Incidental Mutation 'R5048:Atg4b'
ID 394440
Institutional Source Beutler Lab
Gene Symbol Atg4b
Ensembl Gene ENSMUSG00000026280
Gene Name autophagy related 4B, cysteine peptidase
Synonyms 2510009N07Rik, autophagin 1, Apg4b
MMRRC Submission 042638-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.098) question?
Stock # R5048 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 93682627-93717328 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 93703380 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 139 (I139T)
Ref Sequence ENSEMBL: ENSMUSP00000027502 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000027502] [ENSMUST00000149436] [ENSMUST00000185482] [ENSMUST00000187824]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000027502
AA Change: I139T

PolyPhen 2 Score 0.746 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000027502
Gene: ENSMUSG00000026280
AA Change: I139T

DomainStartEndE-ValueType
Pfam:Peptidase_C54 39 335 4.4e-104 PFAM
low complexity region 375 393 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135762
Predicted Effect probably benign
Transcript: ENSMUST00000149436
AA Change: I142T

PolyPhen 2 Score 0.127 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000123383
Gene: ENSMUSG00000026280
AA Change: I142T

DomainStartEndE-ValueType
Pfam:Peptidase_C54 42 150 6.9e-49 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000185482
SMART Domains Protein: ENSMUSP00000140758
Gene: ENSMUSG00000026280

DomainStartEndE-ValueType
Pfam:Peptidase_C54 36 137 2.3e-39 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000186001
Predicted Effect possibly damaging
Transcript: ENSMUST00000187824
AA Change: I106T

PolyPhen 2 Score 0.633 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000139541
Gene: ENSMUSG00000026280
AA Change: I106T

DomainStartEndE-ValueType
Pfam:Peptidase_C54 61 121 1.5e-16 PFAM
Meta Mutation Damage Score 0.3236 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.2%
  • 20x: 92.1%
Validation Efficiency 98% (64/65)
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 encodes a member of the autophagin protein family. The encoded protein is also designated as a member of the C-54 family of cysteine proteases. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a gene trap allele exhibit decreased autophagy, impaired swimming, circling, head tilting, and abnormal utricle, saccular, and otolith morphology. Mice homozygous for another gene trap allele exhibit partial preweaning lethality and impaired motor coordination and learning. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb11 T C 2: 69,138,850 (GRCm39) I144V probably benign Het
Abhd5 T C 9: 122,206,968 (GRCm39) Y85H probably damaging Het
Acadsb G A 7: 131,039,198 (GRCm39) G323D probably damaging Het
Amotl2 A G 9: 102,600,997 (GRCm39) R322G probably benign Het
Aox1 A T 1: 58,098,641 (GRCm39) probably benign Het
Aste1 C T 9: 105,274,188 (GRCm39) R82W probably damaging Het
Btnl5-ps T A 17: 34,707,697 (GRCm39) noncoding transcript Het
Ccdc85c A G 12: 108,187,966 (GRCm39) probably null Het
Clasp1 A G 1: 118,475,340 (GRCm39) probably benign Het
Defb10 G A 8: 22,351,887 (GRCm39) C44Y probably damaging Het
Dhrs9 T C 2: 69,224,744 (GRCm39) V144A probably damaging Het
Dnhd1 G C 7: 105,342,904 (GRCm39) S1416T probably benign Het
Dok1 T A 6: 83,009,087 (GRCm39) probably benign Het
Emilin2 G A 17: 71,580,962 (GRCm39) T588M probably damaging Het
Fam181b A G 7: 92,729,147 (GRCm39) probably benign Het
Fhad1 T C 4: 141,691,987 (GRCm39) probably null Het
Foxi2 A G 7: 135,013,364 (GRCm39) E198G probably damaging Het
Fsip2 C A 2: 82,823,494 (GRCm39) A6409E probably damaging Het
Gje1 T C 10: 14,593,021 (GRCm39) Y65C probably damaging Het
Gm6401 T C 14: 41,789,724 (GRCm39) probably null Het
Gprc5c T C 11: 114,761,177 (GRCm39) *442Q probably null Het
Iars1 T A 13: 49,841,713 (GRCm39) I67N probably damaging Het
Igkv4-79 T C 6: 69,019,971 (GRCm39) S115G probably benign Het
Itga4 C A 2: 79,103,378 (GRCm39) S156R probably benign Het
Lilra6 C T 7: 3,918,440 (GRCm39) probably null Het
Majin C A 19: 6,272,684 (GRCm39) A208E probably benign Het
Megf8 A G 7: 25,030,517 (GRCm39) Q490R possibly damaging Het
Mfng C T 15: 78,648,588 (GRCm39) R163H probably benign Het
Mgarp G A 3: 51,298,707 (GRCm39) R88C probably damaging Het
Msh2 T C 17: 87,980,196 (GRCm39) F58S probably damaging Het
Nemp1 T C 10: 127,526,804 (GRCm39) probably null Het
Nlrp10 A T 7: 108,523,772 (GRCm39) N569K probably benign Het
Nxpe2 T C 9: 48,237,388 (GRCm39) probably null Het
Or4c106 T C 2: 88,682,807 (GRCm39) V171A possibly damaging Het
Or5w16 C A 2: 87,576,663 (GRCm39) A41E probably benign Het
Pdcd11 C A 19: 47,095,554 (GRCm39) S625R probably benign Het
Pigb T A 9: 72,936,990 (GRCm39) probably null Het
Pitpnb T C 5: 111,530,869 (GRCm39) F221L possibly damaging Het
Prox2 A T 12: 85,141,115 (GRCm39) W363R probably damaging Het
Psmg1 T A 16: 95,785,171 (GRCm39) R139S probably benign Het
Rab11fip3 A G 17: 26,286,554 (GRCm39) probably null Het
Samd9l G A 6: 3,374,157 (GRCm39) R1035C probably benign Het
Shkbp1 G A 7: 27,051,521 (GRCm39) probably benign Het
Slc30a5 C A 13: 100,943,249 (GRCm39) L536F probably damaging Het
Slc6a17 A T 3: 107,378,753 (GRCm39) L643* probably null Het
Slit3 T C 11: 35,479,812 (GRCm39) Y330H probably damaging Het
St13 G C 15: 81,283,786 (GRCm39) R4G probably benign Het
Stoml3 A C 3: 53,408,213 (GRCm39) K86N possibly damaging Het
Tmtc1 A T 6: 148,139,344 (GRCm39) L926Q possibly damaging Het
Tns4 T G 11: 98,969,605 (GRCm39) R285S possibly damaging Het
Uncx C T 5: 139,532,874 (GRCm39) T313M probably benign Het
Vmn2r75 G A 7: 85,814,735 (GRCm39) R253C possibly damaging Het
Zbed6 T C 1: 133,586,462 (GRCm39) S292G probably damaging Het
Zfp143 A G 7: 109,673,325 (GRCm39) T142A probably damaging Het
Zfp287 T C 11: 62,605,777 (GRCm39) K366E probably damaging Het
Other mutations in Atg4b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01832:Atg4b APN 1 93,713,626 (GRCm39) splice site probably benign
IGL01875:Atg4b APN 1 93,706,032 (GRCm39) missense probably damaging 1.00
IGL02884:Atg4b APN 1 93,715,437 (GRCm39) utr 3 prime probably benign
R0050:Atg4b UTSW 1 93,715,440 (GRCm39) utr 3 prime probably benign
R0050:Atg4b UTSW 1 93,715,440 (GRCm39) utr 3 prime probably benign
R0387:Atg4b UTSW 1 93,714,278 (GRCm39) missense probably benign 0.02
R0533:Atg4b UTSW 1 93,712,632 (GRCm39) splice site probably benign
R2382:Atg4b UTSW 1 93,712,564 (GRCm39) missense probably damaging 1.00
R3113:Atg4b UTSW 1 93,703,426 (GRCm39) splice site probably benign
R3730:Atg4b UTSW 1 93,695,997 (GRCm39) missense probably damaging 0.99
R4303:Atg4b UTSW 1 93,695,984 (GRCm39) missense probably benign 0.02
R4612:Atg4b UTSW 1 93,714,263 (GRCm39) missense probably damaging 1.00
R5027:Atg4b UTSW 1 93,714,297 (GRCm39) missense probably benign 0.00
R5427:Atg4b UTSW 1 93,702,928 (GRCm39) missense probably damaging 1.00
R5735:Atg4b UTSW 1 93,701,519 (GRCm39) missense probably damaging 1.00
R7209:Atg4b UTSW 1 93,702,955 (GRCm39) missense probably damaging 1.00
R8194:Atg4b UTSW 1 93,713,694 (GRCm39) nonsense probably null
R8214:Atg4b UTSW 1 93,712,609 (GRCm39) missense probably damaging 1.00
R8724:Atg4b UTSW 1 93,696,023 (GRCm39) missense probably damaging 0.99
R8949:Atg4b UTSW 1 93,715,479 (GRCm39) makesense probably null
R8987:Atg4b UTSW 1 93,706,081 (GRCm39) missense possibly damaging 0.54
R9357:Atg4b UTSW 1 93,713,648 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GAGTTAGGCTCCTCTTGGAAGG -3'
(R):5'- GAACAATTGGCATAGTCACCCAG -3'

Sequencing Primer
(F):5'- AGGCTCCTCTTGGAAGGTTTGC -3'
(R):5'- ATTGGCATAGTCACCCAGGGATC -3'
Posted On 2016-06-15