Incidental Mutation 'R7898:Afg2a'
ID 609802
Institutional Source Beutler Lab
Gene Symbol Afg2a
Ensembl Gene ENSMUSG00000027722
Gene Name AFG2 AAA ATPase homolog A
Synonyms 2510048F20Rik, Spata5, C78064, Spaf
MMRRC Submission 045950-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7898 (G1)
Quality Score 88.0076
Status Validated
Chromosome 3
Chromosomal Location 37474052-37633245 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 37474620 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Arginine at position 44 (M44R)
Ref Sequence ENSEMBL: ENSMUSP00000103747 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029277] [ENSMUST00000052645] [ENSMUST00000099130] [ENSMUST00000108112] [ENSMUST00000108117] [ENSMUST00000108118] [ENSMUST00000141438] [ENSMUST00000146324] [ENSMUST00000149449] [ENSMUST00000198968]
AlphaFold Q3UMC0
Predicted Effect probably benign
Transcript: ENSMUST00000029277
AA Change: M44R

PolyPhen 2 Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000029277
Gene: ENSMUSG00000027722
AA Change: M44R

DomainStartEndE-ValueType
low complexity region 12 26 N/A INTRINSIC
CDC48_N 44 135 2.47e-1 SMART
low complexity region 276 287 N/A INTRINSIC
AAA 385 524 4.96e-21 SMART
Blast:AAA 553 622 9e-21 BLAST
AAA 659 797 2.48e-21 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000052645
SMART Domains Protein: ENSMUSP00000056219
Gene: ENSMUSG00000050174

DomainStartEndE-ValueType
PDB:3FXT|H 42 131 1e-42 PDB
Pfam:NUDIX 139 270 2.7e-23 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000099130
SMART Domains Protein: ENSMUSP00000096733
Gene: ENSMUSG00000050174

DomainStartEndE-ValueType
PDB:3FXT|H 42 131 1e-42 PDB
Pfam:NUDIX 139 269 7.3e-22 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000108112
AA Change: M44R

PolyPhen 2 Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000103747
Gene: ENSMUSG00000027722
AA Change: M44R

DomainStartEndE-ValueType
low complexity region 12 26 N/A INTRINSIC
CDC48_N 44 136 1.14e0 SMART
low complexity region 277 288 N/A INTRINSIC
AAA 386 525 4.96e-21 SMART
Blast:AAA 554 623 9e-21 BLAST
AAA 660 798 2.48e-21 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000108117
SMART Domains Protein: ENSMUSP00000103752
Gene: ENSMUSG00000050174

DomainStartEndE-ValueType
PDB:3FXT|H 42 76 3e-7 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000108118
SMART Domains Protein: ENSMUSP00000103753
Gene: ENSMUSG00000050174

DomainStartEndE-ValueType
Pfam:NUDIX 73 202 1.7e-22 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000138949
SMART Domains Protein: ENSMUSP00000118428
Gene: ENSMUSG00000050174

DomainStartEndE-ValueType
PDB:3FXT|H 17 98 4e-30 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000141438
SMART Domains Protein: ENSMUSP00000142588
Gene: ENSMUSG00000050174

DomainStartEndE-ValueType
PDB:3H95|A 2 97 5e-55 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000146324
SMART Domains Protein: ENSMUSP00000142653
Gene: ENSMUSG00000050174

DomainStartEndE-ValueType
Pfam:NUDIX 1 104 6.6e-17 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000149449
SMART Domains Protein: ENSMUSP00000116572
Gene: ENSMUSG00000050174

DomainStartEndE-ValueType
PDB:3FXT|H 42 131 3e-44 PDB
PDB:3H95|A 132 191 6e-22 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000198158
Predicted Effect probably benign
Transcript: ENSMUST00000198968
AA Change: M44R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000143349
Gene: ENSMUSG00000027722
AA Change: M44R

DomainStartEndE-ValueType
low complexity region 12 26 N/A INTRINSIC
CDC48_N 44 136 8.6e-5 SMART
low complexity region 277 288 N/A INTRINSIC
AAA 386 525 8.2e-23 SMART
Blast:AAA 554 623 7e-21 BLAST
AAA 660 798 4e-23 SMART
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 99% (69/70)
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 ATPase associated with diverse activities family, whose members are defined by a highly conserved ATPase domain. Members of this family participate in diverse cellular processes that include membrane fusion, DNA replication, microtubule severing, and protein degradation. The protein encoded by this gene has a putative mitochondrial targeting sequence and has been proposed to function in maintenance of mitochondrial function and integrity during mouse spermatogenesis. Allelic variants in this gene have been associated with epilepsy, hearing loss, and mental retardation syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acaca T C 11: 84,255,275 (GRCm39) probably null Het
Ankef1 C A 2: 136,395,618 (GRCm39) N649K probably benign Het
Arl5b T A 2: 15,079,869 (GRCm39) S147T probably damaging Het
Arnt2 A T 7: 83,918,155 (GRCm39) probably null Het
Ash1l A G 3: 88,890,932 (GRCm39) E937G possibly damaging Het
Asxl1 T G 2: 153,241,854 (GRCm39) S802R possibly damaging Het
Cacna1h T A 17: 25,611,250 (GRCm39) H516L probably damaging Het
Cad A G 5: 31,218,829 (GRCm39) Y550C probably damaging Het
Cdo1 A G 18: 46,861,157 (GRCm39) I18T probably benign Het
Cfap251 A T 5: 123,460,517 (GRCm39) I1160F probably damaging Het
Chd2 A G 7: 73,169,223 (GRCm39) probably null Het
Dbf4 A G 5: 8,458,232 (GRCm39) probably null Het
Dcdc2a A T 13: 25,286,361 (GRCm39) R132W possibly damaging Het
Dnah10 T C 5: 124,859,425 (GRCm39) S2131P probably damaging Het
Eef2k A G 7: 120,494,441 (GRCm39) Y599C probably damaging Het
Eno2 C T 6: 124,744,225 (GRCm39) probably null Het
Fam124b T A 1: 80,191,512 (GRCm39) probably benign Het
Fezf2 A G 14: 12,342,701 (GRCm38) I388T possibly damaging Het
Gbp11 T C 5: 105,472,798 (GRCm39) N542S probably benign Het
Gdpd1 T A 11: 86,932,639 (GRCm39) I229F probably damaging Het
Gria1 T A 11: 57,133,591 (GRCm39) V490E probably damaging Het
Grm8 G A 6: 27,762,422 (GRCm39) R268C probably damaging Het
Hectd4 T A 5: 121,469,880 (GRCm39) S2592T probably benign Het
Herpud1 C T 8: 95,118,828 (GRCm39) T194I probably benign Het
Hspa1b T C 17: 35,177,167 (GRCm39) T273A probably benign Het
Iftap T A 2: 101,416,747 (GRCm39) K67N probably benign Het
Ighm T A 12: 113,384,873 (GRCm39) K327* probably null Het
Igkv3-4 A T 6: 70,649,297 (GRCm39) I99F probably damaging Het
Iqca1l T C 5: 24,758,643 (GRCm39) E117G probably damaging Het
Isl2 C A 9: 55,449,723 (GRCm39) S97R probably benign Het
Klhl12 A T 1: 134,386,219 (GRCm39) I4F probably benign Het
Lgalsl2 G A 7: 5,362,441 (GRCm39) R24H probably benign Het
Lrp2 T C 2: 69,271,710 (GRCm39) E4074G probably benign Het
Mcm3ap A G 10: 76,342,441 (GRCm39) N1645D probably damaging Het
Mettl23 T C 11: 116,736,679 (GRCm39) probably benign Het
Mettl24 A G 10: 40,686,478 (GRCm39) E285G probably benign Het
Mis18bp1 A G 12: 65,196,246 (GRCm39) L506P probably benign Het
Mup18 G T 4: 61,590,925 (GRCm39) probably null Het
Myom1 T C 17: 71,352,747 (GRCm39) L357P probably benign Het
Nkx2-9 G A 12: 56,659,031 (GRCm39) A61V probably benign Het
Or52n5 C T 7: 104,588,573 (GRCm39) A280V probably damaging Het
Pbx1 A T 1: 168,012,616 (GRCm39) M340K probably benign Het
Pcdhb17 A T 18: 37,618,233 (GRCm39) N8Y probably benign Het
Pex13 C A 11: 23,600,929 (GRCm39) probably null Het
Pierce1 TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC 2: 28,356,122 (GRCm39) probably benign Het
Plxnb1 A G 9: 108,943,408 (GRCm39) R1884G probably damaging Het
Polq T A 16: 36,865,245 (GRCm39) V699E probably damaging Het
Ppl C T 16: 4,906,725 (GRCm39) R1190H probably damaging Het
Prr14l A T 5: 32,987,310 (GRCm39) H728Q probably benign Het
Prss12 T C 3: 123,300,145 (GRCm39) V752A possibly damaging Het
Prss56 A G 1: 87,111,921 (GRCm39) S51G probably benign Het
Pwp2 G A 10: 78,009,240 (GRCm39) R854W probably damaging Het
Rhobtb2 C T 14: 70,033,746 (GRCm39) C493Y probably damaging Het
Rictor C T 15: 6,801,635 (GRCm39) S441L probably benign Het
Rusf1 C A 7: 127,897,177 (GRCm39) A27S probably benign Het
Scap A G 9: 110,213,811 (GRCm39) N1258S possibly damaging Het
Sec31a C T 5: 100,547,336 (GRCm39) G218R probably damaging Het
Siglec15 A T 18: 78,086,914 (GRCm39) M315K probably benign Het
Slc17a6 G A 7: 51,308,573 (GRCm39) probably null Het
Smchd1 T C 17: 71,684,813 (GRCm39) probably null Het
Spag4 A T 2: 155,911,244 (GRCm39) D393V probably damaging Het
Sulf1 A G 1: 12,875,518 (GRCm39) N176S probably damaging Het
Tmem9 T A 1: 135,955,125 (GRCm39) probably null Het
Tnpo3 T C 6: 29,565,223 (GRCm39) I577V probably benign Het
Tti1 A C 2: 157,835,390 (GRCm39) I956S probably benign Het
Wdr81 T C 11: 75,344,725 (GRCm39) R181G probably benign Het
Zfp462 T A 4: 55,012,995 (GRCm39) C1654S probably damaging Het
Zfp74 A T 7: 29,635,380 (GRCm39) C109* probably null Het
Znrf4 A G 17: 56,818,681 (GRCm39) C209R probably damaging Het
Zzef1 T G 11: 72,687,373 (GRCm39) L84R probably damaging Het
Other mutations in Afg2a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00417:Afg2a APN 3 37,505,951 (GRCm39) missense possibly damaging 0.60
IGL00472:Afg2a APN 3 37,490,793 (GRCm39) missense probably benign
IGL02664:Afg2a APN 3 37,490,814 (GRCm39) missense probably damaging 1.00
IGL02797:Afg2a APN 3 37,512,465 (GRCm39) splice site probably benign
IGL02869:Afg2a APN 3 37,518,694 (GRCm39) missense probably damaging 1.00
IGL02891:Afg2a APN 3 37,480,341 (GRCm39) missense probably damaging 0.97
IGL03065:Afg2a APN 3 37,486,328 (GRCm39) missense possibly damaging 0.75
IGL03121:Afg2a APN 3 37,518,800 (GRCm39) missense probably damaging 1.00
IGL03178:Afg2a APN 3 37,632,932 (GRCm39) missense probably damaging 1.00
R0494:Afg2a UTSW 3 37,486,312 (GRCm39) missense possibly damaging 0.79
R0621:Afg2a UTSW 3 37,486,178 (GRCm39) missense probably benign 0.06
R0908:Afg2a UTSW 3 37,485,772 (GRCm39) splice site probably null
R1773:Afg2a UTSW 3 37,493,334 (GRCm39) missense probably damaging 0.99
R2016:Afg2a UTSW 3 37,632,911 (GRCm39) missense possibly damaging 0.48
R3714:Afg2a UTSW 3 37,487,358 (GRCm39) missense probably benign
R3836:Afg2a UTSW 3 37,487,792 (GRCm39) missense possibly damaging 0.91
R4548:Afg2a UTSW 3 37,486,176 (GRCm39) missense probably benign 0.03
R4695:Afg2a UTSW 3 37,512,474 (GRCm39) missense probably damaging 1.00
R4758:Afg2a UTSW 3 37,487,385 (GRCm39) missense probably benign 0.01
R5009:Afg2a UTSW 3 37,487,426 (GRCm39) splice site probably benign
R5839:Afg2a UTSW 3 37,518,803 (GRCm39) missense probably damaging 1.00
R6437:Afg2a UTSW 3 37,582,347 (GRCm39) missense probably damaging 1.00
R7067:Afg2a UTSW 3 37,485,847 (GRCm39) nonsense probably null
R7450:Afg2a UTSW 3 37,510,934 (GRCm39) missense probably damaging 1.00
R7889:Afg2a UTSW 3 37,632,959 (GRCm39) missense probably benign 0.01
R8108:Afg2a UTSW 3 37,485,931 (GRCm39) missense probably benign 0.25
R8511:Afg2a UTSW 3 37,490,897 (GRCm39) missense probably damaging 0.99
R8870:Afg2a UTSW 3 37,502,661 (GRCm39) missense probably benign 0.35
R8941:Afg2a UTSW 3 37,486,142 (GRCm39) missense probably damaging 0.97
R9475:Afg2a UTSW 3 37,486,058 (GRCm39) missense probably benign
R9605:Afg2a UTSW 3 37,505,930 (GRCm39) missense probably damaging 1.00
Z1176:Afg2a UTSW 3 37,485,899 (GRCm39) missense possibly damaging 0.67
Predicted Primers PCR Primer
(F):5'- TCTGACCCGGAAGTTTGATCC -3'
(R):5'- GCTCCCGAAGTACGTATGAAAG -3'

Sequencing Primer
(F):5'- AAGTTTGATCCCCGTGCCG -3'
(R):5'- AAAAGGCAATCCTCAACTTTTTGC -3'
Posted On 2019-12-20