Incidental Mutation 'G5030:Pex6'
| ID |
485 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pex6
|
| Ensembl Gene |
ENSMUSG00000002763 |
| Gene Name |
peroxisomal biogenesis factor 6 |
| Synonyms |
D130055I09Rik |
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.864)
|
| Stock # |
G5030 (G3)
of strain
560
|
| Quality Score |
|
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
47022402-47036469 bp(+) (GRCm39) |
| Type of Mutation |
intron |
| DNA Base Change (assembly) |
T to C
at 47026382 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000002840
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000002840]
|
| AlphaFold |
Q99LC9 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000002840
|
| SMART Domains |
Protein: ENSMUSP00000002840
Gene: ENSMUSG00000002763
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
17 |
31 |
N/A |
INTRINSIC |
|
low complexity region
|
72 |
86 |
N/A |
INTRINSIC |
|
low complexity region
|
87 |
104 |
N/A |
INTRINSIC |
|
low complexity region
|
112 |
128 |
N/A |
INTRINSIC |
|
low complexity region
|
173 |
200 |
N/A |
INTRINSIC |
|
AAA
|
463 |
598 |
6.1e-7 |
SMART |
|
AAA
|
737 |
875 |
6e-24 |
SMART |
|
Blast:AAA
|
928 |
973 |
1e-14 |
BLAST |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000127897
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144964
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148872
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000181301
|
| Coding Region Coverage |
|
| Het Detection Efficiency |
35.6% |
| Validation Efficiency |
87% (206/237) |
| 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 AAA (ATPases associated with diverse cellular activities) family of ATPases. This member is a predominantly cytoplasmic protein, which plays a direct role in peroxisomal protein import and is required for PTS1 (peroxisomal targeting signal 1, a C-terminal tripeptide of the sequence ser-lys-leu) receptor activity. Mutations in this gene cause peroxisome biogenesis disorders of complementation group 4 and complementation group 6. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 30 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca8a |
T |
A |
11: 109,961,165 (GRCm39) |
I585F |
probably damaging |
Het |
| Adam18 |
C |
G |
8: 25,141,872 (GRCm39) |
L232F |
probably benign |
Homo |
| Atp13a4 |
A |
G |
16: 29,274,306 (GRCm39) |
I385T |
probably damaging |
Homo |
| Ccdc17 |
T |
A |
4: 116,455,699 (GRCm39) |
S277T |
probably benign |
Het |
| Ccng1 |
A |
G |
11: 40,644,629 (GRCm39) |
|
probably benign |
Het |
| Ces1f |
T |
C |
8: 94,000,847 (GRCm39) |
D99G |
probably benign |
Het |
| Clec16a |
G |
A |
16: 10,389,425 (GRCm39) |
R187Q |
probably damaging |
Homo |
| Cryl1 |
C |
T |
14: 57,579,595 (GRCm39) |
|
probably benign |
Het |
| Cryzl2 |
C |
T |
1: 157,292,580 (GRCm39) |
Q48* |
probably null |
Het |
| Dtx4 |
A |
G |
19: 12,446,943 (GRCm39) |
L583P |
probably benign |
Het |
| Ephx4 |
A |
T |
5: 107,577,693 (GRCm39) |
D339V |
probably damaging |
Het |
| Eri2 |
A |
T |
7: 119,385,601 (GRCm39) |
V300E |
possibly damaging |
Het |
| F3 |
T |
A |
3: 121,518,648 (GRCm39) |
N37K |
probably damaging |
Homo |
| Fpr1 |
A |
T |
17: 18,097,068 (GRCm39) |
L307H |
probably damaging |
Het |
| Fv1 |
T |
A |
4: 147,953,618 (GRCm39) |
N61K |
possibly damaging |
Het |
| Gm5548 |
T |
C |
3: 112,961,512 (GRCm39) |
|
noncoding transcript |
Homo |
| Il1r1 |
A |
G |
1: 40,352,323 (GRCm39) |
K498E |
possibly damaging |
Homo |
| Myh11 |
T |
C |
16: 14,068,443 (GRCm39) |
I192M |
probably damaging |
Homo |
| Nckap5 |
T |
C |
1: 125,953,591 (GRCm39) |
K923R |
probably damaging |
Het |
| Nmbr |
A |
T |
10: 14,642,747 (GRCm39) |
Y102F |
possibly damaging |
Het |
| Or6c75 |
A |
G |
10: 129,337,406 (GRCm39) |
T218A |
probably benign |
Homo |
| Pde1a |
C |
T |
2: 79,718,180 (GRCm39) |
|
probably benign |
Het |
| Rtn2 |
T |
C |
7: 19,027,099 (GRCm39) |
S305P |
probably damaging |
Homo |
| Saal1 |
G |
A |
7: 46,342,207 (GRCm39) |
T412I |
probably damaging |
Homo |
| Slc46a2 |
A |
T |
4: 59,913,867 (GRCm39) |
I352N |
probably damaging |
Het |
| Trim37 |
A |
T |
11: 87,033,967 (GRCm39) |
H99L |
probably damaging |
Het |
| Tubgcp4 |
C |
T |
2: 121,014,815 (GRCm39) |
R242C |
probably damaging |
Het |
| Twf2 |
C |
A |
9: 106,084,141 (GRCm39) |
L27I |
possibly damaging |
Het |
| Usp40 |
A |
T |
1: 87,921,941 (GRCm39) |
H307Q |
probably damaging |
Het |
| Zfhx3 |
T |
G |
8: 109,678,091 (GRCm39) |
V3047G |
possibly damaging |
Het |
|
| Other mutations in Pex6 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01478:Pex6
|
APN |
17 |
47,036,230 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01601:Pex6
|
APN |
17 |
47,034,650 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01710:Pex6
|
APN |
17 |
47,036,252 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02392:Pex6
|
APN |
17 |
47,034,425 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02419:Pex6
|
APN |
17 |
47,035,361 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R0091:Pex6
|
UTSW |
17 |
47,022,844 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0243:Pex6
|
UTSW |
17 |
47,034,663 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0732:Pex6
|
UTSW |
17 |
47,035,626 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1529:Pex6
|
UTSW |
17 |
47,024,990 (GRCm39) |
missense |
probably benign |
0.10 |
|
R1602:Pex6
|
UTSW |
17 |
47,023,063 (GRCm39) |
missense |
probably benign |
0.09 |
|
R1638:Pex6
|
UTSW |
17 |
47,033,558 (GRCm39) |
missense |
probably benign |
|
|
R1757:Pex6
|
UTSW |
17 |
47,034,424 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3769:Pex6
|
UTSW |
17 |
47,035,311 (GRCm39) |
splice site |
probably null |
|
|
R4684:Pex6
|
UTSW |
17 |
47,023,027 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4731:Pex6
|
UTSW |
17 |
47,035,633 (GRCm39) |
splice site |
probably null |
|
|
R4731:Pex6
|
UTSW |
17 |
47,033,214 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4732:Pex6
|
UTSW |
17 |
47,033,214 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4732:Pex6
|
UTSW |
17 |
47,035,633 (GRCm39) |
splice site |
probably null |
|
|
R4733:Pex6
|
UTSW |
17 |
47,035,633 (GRCm39) |
splice site |
probably null |
|
|
R4733:Pex6
|
UTSW |
17 |
47,033,214 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4915:Pex6
|
UTSW |
17 |
47,024,982 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R5996:Pex6
|
UTSW |
17 |
47,025,384 (GRCm39) |
splice site |
probably null |
|
|
R6156:Pex6
|
UTSW |
17 |
47,031,567 (GRCm39) |
missense |
probably benign |
0.02 |
|
R6227:Pex6
|
UTSW |
17 |
47,023,034 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7054:Pex6
|
UTSW |
17 |
47,031,447 (GRCm39) |
missense |
probably benign |
|
|
R7635:Pex6
|
UTSW |
17 |
47,034,943 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8034:Pex6
|
UTSW |
17 |
47,033,325 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
R8177:Pex6
|
UTSW |
17 |
47,024,988 (GRCm39) |
missense |
probably benign |
|
|
R8330:Pex6
|
UTSW |
17 |
47,023,060 (GRCm39) |
missense |
possibly damaging |
0.55 |
|
R8348:Pex6
|
UTSW |
17 |
47,034,039 (GRCm39) |
missense |
probably benign |
|
|
R8695:Pex6
|
UTSW |
17 |
47,022,975 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R9263:Pex6
|
UTSW |
17 |
47,023,231 (GRCm39) |
missense |
probably benign |
0.16 |
|
R9428:Pex6
|
UTSW |
17 |
47,022,991 (GRCm39) |
missense |
probably benign |
|
|
R9600:Pex6
|
UTSW |
17 |
47,035,322 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1088:Pex6
|
UTSW |
17 |
47,023,148 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
| Nature of Mutation |
 DNA sequencing using the SOLiD technique identified a T to C transition at position 1246 of the Pex6 transcript using Ensembl record ENSMUST00000066348 in exon 4 of 4 total exons. According to the Genbank record, the Pex6 gene contains 17 total exons. The cDNA of this Ensembl record only partially matches the Genbank record and the altered base pair is located only in the Ensembl record. Multiple transcripts of the Pex6 gene are displayed on Ensembl and Vega. The mutated nucleotide causes a cysteine to arginine substitution at amino acid 410 of the encoded protein. The mutation has been confirmed by DNA sequencing using the Sanger method (Figure 1).
|
| Protein Function and Prediction |
The Pex6 gene encodes a 981 amino acid protein that is a member of the AAA ATPase family and is involved in peroxisome biosynthesis. PEX6 plays a role in protein import into peroxisomes. ATP binding occurs at residues 471-478 and 745-752 (Uniprot Q99LC9). In humans, mutations in the PEX6 gene cause peroxisomal biogenesis disorders (PBDs; OMIM 601539).
The protein encoded by the Ensembl record only matches the first 378 amino acids of the annotated PEX6 protein. The C410R change occurs outside this region and may be translated from an intron. It is predicted to be benign by the PolyPhen program . |
| Posted On |
2010-10-27 |
Incidental Mutation