Incidental Mutation 'RF021:Vps16'
| ID |
603862 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps16
|
| Ensembl Gene |
ENSMUSG00000027411 |
| Gene Name |
VSP16 CORVET/HOPS core subunit |
| Synonyms |
1810074M16Rik |
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.970)
|
| Stock # |
RF021 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
130266259-130286189 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 130280129 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Arginine
at position 118
(H118R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000028900
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028900]
[ENSMUST00000128994]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000028900
AA Change: H118R
PolyPhen 2
Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: H118R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Vps16_N
|
4 |
420 |
1e-166 |
PFAM |
|
low complexity region
|
452 |
462 |
N/A |
INTRINSIC |
|
Pfam:Vps16_C
|
517 |
835 |
5.5e-150 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000128994
AA Change: H118R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000115899
Gene: ENSMUSG00000027411
AA Change: H118R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Vps16_N
|
4 |
212 |
3.2e-74 |
PFAM |
|
Pfam:Vps16_N
|
205 |
316 |
1e-45 |
PFAM |
|
| Coding Region Coverage |
- 1x: 99.8%
- 3x: 99.7%
- 10x: 99.3%
- 20x: 98.3%
|
| Validation Efficiency |
91% (50/55) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps16 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]
PHENOTYPE: Mice with a homozygous point mutation in exon 3 display impaired motor function. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A030005L19Rik |
GTGGTGGCTG |
GTGGTGGCTGTGGTGGCTG |
1: 82,891,290 (GRCm39) |
|
probably benign |
Het |
| AI837181 |
CGG |
CGGTGG |
19: 5,475,262 (GRCm39) |
|
probably benign |
Het |
| Ankrd44 |
T |
C |
1: 54,817,471 (GRCm39) |
H79R |
probably damaging |
Het |
| Atg9a |
T |
A |
1: 75,159,273 (GRCm39) |
E826V |
probably damaging |
Het |
| Atrnl1 |
T |
C |
19: 57,630,905 (GRCm39) |
V224A |
probably benign |
Het |
| Bltp1 |
TTATTATTATTAT |
TTATTATTATTATTAATATTATTATTAT |
3: 37,104,897 (GRCm39) |
|
probably benign |
Het |
| Cpn2 |
G |
A |
16: 30,078,156 (GRCm39) |
A515V |
probably benign |
Het |
| Cyp2a12 |
T |
C |
7: 26,734,785 (GRCm39) |
F402S |
possibly damaging |
Het |
| Defb22 |
TGCGGCA |
TGCGGCAGAGCTGGGCGTTGCGGCA |
2: 152,327,752 (GRCm39) |
|
probably benign |
Het |
| Dnah10 |
G |
T |
5: 124,854,971 (GRCm39) |
V2016F |
probably damaging |
Het |
| Dock10 |
T |
C |
1: 80,542,290 (GRCm39) |
|
probably null |
Het |
| Efhd2 |
GCC |
GCCGCCCCC |
4: 141,602,084 (GRCm39) |
|
probably benign |
Het |
| Fam131a |
A |
C |
16: 20,513,690 (GRCm39) |
|
probably benign |
Het |
| Gm7247 |
AGACCAGACC |
A |
14: 51,601,781 (GRCm39) |
|
probably benign |
Het |
| Gna13 |
T |
C |
11: 109,283,218 (GRCm39) |
V186A |
probably benign |
Het |
| Grk3 |
T |
A |
5: 113,089,554 (GRCm39) |
I333L |
probably benign |
Het |
| Gstp1 |
A |
T |
19: 4,085,507 (GRCm39) |
V200E |
probably benign |
Het |
| Gtf2h1 |
T |
G |
7: 46,453,289 (GRCm39) |
V74G |
possibly damaging |
Het |
| Kcnh8 |
G |
A |
17: 53,285,267 (GRCm39) |
R1079H |
probably benign |
Het |
| Kiz |
A |
G |
2: 146,712,750 (GRCm39) |
D138G |
possibly damaging |
Het |
| Kmt2b |
TTCTCCT |
TTCTCCTTCTCCT |
7: 30,285,782 (GRCm39) |
|
probably benign |
Het |
| Lats1 |
A |
G |
10: 7,586,372 (GRCm39) |
T912A |
probably damaging |
Het |
| Lce1m |
GCTGCCACC |
GCTGCCACCACTTCTGCCACC |
3: 92,925,576 (GRCm39) |
|
probably benign |
Het |
| Lce1m |
TGCC |
TGCCGCCGCTGCCGCC |
3: 92,925,602 (GRCm39) |
|
probably benign |
Het |
| Lrrc2 |
TTGATTCGGTTCACC |
T |
9: 110,810,744 (GRCm39) |
|
probably null |
Het |
| Med12l |
T |
C |
3: 58,980,711 (GRCm39) |
F359S |
probably benign |
Het |
| Mmut |
A |
G |
17: 41,262,649 (GRCm39) |
I444V |
probably benign |
Het |
| Ncoa2 |
CTTAAAA |
C |
1: 13,219,333 (GRCm39) |
|
probably benign |
Het |
| Ngp |
A |
G |
9: 110,250,824 (GRCm39) |
T114A |
possibly damaging |
Het |
| Nlrc5 |
A |
T |
8: 95,203,516 (GRCm39) |
T539S |
probably benign |
Het |
| Nxf1 |
A |
G |
19: 8,749,673 (GRCm39) |
D190G |
probably damaging |
Het |
| Or6c2b |
A |
T |
10: 128,948,211 (GRCm39) |
F28I |
probably damaging |
Het |
| Or8g2 |
A |
T |
9: 39,821,341 (GRCm39) |
M81L |
probably benign |
Het |
| Pramel16 |
C |
G |
4: 143,675,478 (GRCm39) |
Q449H |
probably damaging |
Het |
| Prdm15 |
G |
A |
16: 97,609,956 (GRCm39) |
H563Y |
probably damaging |
Het |
| Rbm12 |
CAGG |
CAGGGATTGCGGGACCTGGTATTGCGGGACCAGG |
2: 155,938,026 (GRCm39) |
|
probably benign |
Het |
| Sema3g |
C |
T |
14: 30,949,798 (GRCm39) |
H660Y |
probably damaging |
Het |
| Slco1a8 |
A |
T |
6: 141,954,440 (GRCm39) |
V31E |
probably damaging |
Het |
| Smarca2 |
AGCAGCAGCAGCAGCAGCAGCA |
AGCAGCAGCAGCAGCAGCAGCAGCAGCA |
19: 26,608,397 (GRCm39) |
|
probably benign |
Het |
| Stpg2 |
A |
T |
3: 138,918,011 (GRCm39) |
|
probably null |
Het |
| Taar7f |
C |
T |
10: 23,926,321 (GRCm39) |
T305M |
possibly damaging |
Het |
| Tbcb |
C |
T |
7: 29,923,771 (GRCm39) |
V208M |
probably damaging |
Het |
| Tenm2 |
T |
A |
11: 35,915,030 (GRCm39) |
Q2169L |
possibly damaging |
Het |
| Tln1 |
A |
G |
4: 43,555,890 (GRCm39) |
V108A |
probably damaging |
Het |
| Tmc8 |
T |
C |
11: 117,674,060 (GRCm39) |
M42T |
probably benign |
Het |
| Trdc |
T |
C |
14: 54,381,660 (GRCm39) |
V115A |
|
Het |
| Ttbk2 |
A |
G |
2: 120,579,115 (GRCm39) |
V669A |
probably benign |
Het |
| Tusc1 |
GCC |
GCCACCACC |
4: 93,223,553 (GRCm39) |
|
probably benign |
Het |
| Utp25 |
A |
G |
1: 192,802,974 (GRCm39) |
F248L |
probably benign |
Het |
| Wdpcp |
T |
A |
11: 21,661,587 (GRCm39) |
C286* |
probably null |
Het |
| Zbed4 |
C |
A |
15: 88,665,439 (GRCm39) |
Y502* |
probably null |
Het |
| Zdbf2 |
T |
A |
1: 63,341,811 (GRCm39) |
N63K |
possibly damaging |
Het |
|
| Other mutations in Vps16 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01327:Vps16
|
APN |
2 |
130,279,616 (GRCm39) |
missense |
probably benign |
0.19 |
|
IGL01400:Vps16
|
APN |
2 |
130,280,273 (GRCm39) |
missense |
possibly damaging |
0.73 |
|
IGL01542:Vps16
|
APN |
2 |
130,280,314 (GRCm39) |
missense |
probably damaging |
0.97 |
|
IGL02011:Vps16
|
APN |
2 |
130,283,399 (GRCm39) |
missense |
probably benign |
0.04 |
|
IGL02192:Vps16
|
APN |
2 |
130,282,852 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL02220:Vps16
|
APN |
2 |
130,283,573 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
IGL02587:Vps16
|
APN |
2 |
130,281,636 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0427:Vps16
|
UTSW |
2 |
130,280,770 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0507:Vps16
|
UTSW |
2 |
130,279,632 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1550:Vps16
|
UTSW |
2 |
130,282,260 (GRCm39) |
missense |
probably benign |
0.09 |
|
R1789:Vps16
|
UTSW |
2 |
130,285,520 (GRCm39) |
missense |
probably benign |
0.42 |
|
R3895:Vps16
|
UTSW |
2 |
130,280,596 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
R3981:Vps16
|
UTSW |
2 |
130,284,514 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R4092:Vps16
|
UTSW |
2 |
130,281,832 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4555:Vps16
|
UTSW |
2 |
130,285,496 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4569:Vps16
|
UTSW |
2 |
130,284,124 (GRCm39) |
missense |
probably benign |
|
|
R4803:Vps16
|
UTSW |
2 |
130,280,030 (GRCm39) |
missense |
probably benign |
0.27 |
|
R4835:Vps16
|
UTSW |
2 |
130,280,220 (GRCm39) |
splice site |
probably benign |
|
|
R5022:Vps16
|
UTSW |
2 |
130,281,372 (GRCm39) |
missense |
probably benign |
0.07 |
|
R5023:Vps16
|
UTSW |
2 |
130,281,372 (GRCm39) |
missense |
probably benign |
0.07 |
|
R5057:Vps16
|
UTSW |
2 |
130,281,372 (GRCm39) |
missense |
probably benign |
0.07 |
|
R5158:Vps16
|
UTSW |
2 |
130,283,199 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5177:Vps16
|
UTSW |
2 |
130,285,288 (GRCm39) |
nonsense |
probably null |
|
|
R5540:Vps16
|
UTSW |
2 |
130,284,305 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5680:Vps16
|
UTSW |
2 |
130,282,244 (GRCm39) |
missense |
possibly damaging |
0.64 |
|
R5689:Vps16
|
UTSW |
2 |
130,281,011 (GRCm39) |
nonsense |
probably null |
|
|
R5690:Vps16
|
UTSW |
2 |
130,281,011 (GRCm39) |
nonsense |
probably null |
|
|
R5926:Vps16
|
UTSW |
2 |
130,285,476 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5992:Vps16
|
UTSW |
2 |
130,266,369 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6135:Vps16
|
UTSW |
2 |
130,280,573 (GRCm39) |
missense |
possibly damaging |
0.57 |
|
R6370:Vps16
|
UTSW |
2 |
130,285,304 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6898:Vps16
|
UTSW |
2 |
130,279,601 (GRCm39) |
missense |
possibly damaging |
0.74 |
|
R7378:Vps16
|
UTSW |
2 |
130,280,099 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7487:Vps16
|
UTSW |
2 |
130,280,977 (GRCm39) |
nonsense |
probably null |
|
|
R7641:Vps16
|
UTSW |
2 |
130,282,448 (GRCm39) |
missense |
probably benign |
0.28 |
|
R7720:Vps16
|
UTSW |
2 |
130,283,623 (GRCm39) |
nonsense |
probably null |
|
|
R8246:Vps16
|
UTSW |
2 |
130,280,793 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8363:Vps16
|
UTSW |
2 |
130,284,161 (GRCm39) |
missense |
probably benign |
0.08 |
|
R9092:Vps16
|
UTSW |
2 |
130,281,593 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9128:Vps16
|
UTSW |
2 |
130,266,319 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R9352:Vps16
|
UTSW |
2 |
130,283,823 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9406:Vps16
|
UTSW |
2 |
130,283,425 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9508:Vps16
|
UTSW |
2 |
130,284,361 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R9800:Vps16
|
UTSW |
2 |
130,282,405 (GRCm39) |
missense |
probably benign |
0.02 |
|
Z1177:Vps16
|
UTSW |
2 |
130,283,346 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- CTATCCCTACTGTGTGATGGGC -3'
(R):5'- TTGAGGTCACCCACATTGGC -3'
Sequencing Primer
(F):5'- CAGGGCTGGCTGATTCTAAG -3'
(R):5'- CATTGGCACTCAGAGTAAAGC -3'
|
| Posted On |
2019-12-04 |
Incidental Mutation