Incidental Mutation 'R2080:Tmem59'
| ID |
229407 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tmem59
|
| Ensembl Gene |
ENSMUSG00000028618 |
| Gene Name |
transmembrane protein 59 |
| Synonyms |
3110046P06Rik, thymic dendritic cell-derived factor 1, D4Ertd20e, 1110001M20Rik, MTDCF1 |
| MMRRC Submission |
040085-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.164)
|
| Stock # |
R2080 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
107178399-107200996 bp(+) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 107178774 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Isoleucine
at position 16
(L16I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000119701
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030361]
[ENSMUST00000030362]
[ENSMUST00000057043]
[ENSMUST00000058585]
[ENSMUST00000106753]
[ENSMUST00000127720]
[ENSMUST00000128123]
[ENSMUST00000154007]
[ENSMUST00000141165]
|
| AlphaFold |
Q9QY73 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030361
AA Change: L16I
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000030361
Gene: ENSMUSG00000028618
AA Change: L16I
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
34 |
N/A |
INTRINSIC |
|
Pfam:BSMAP
|
72 |
256 |
1.1e-72 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030362
|
| SMART Domains |
Protein: ENSMUSP00000030362
Gene: ENSMUSG00000028619
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Med26
|
60 |
111 |
7.9e-20 |
PFAM |
|
Pfam:TFIIS_M
|
126 |
207 |
1.7e-8 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000057043
|
| SMART Domains |
Protein: ENSMUSP00000059741
Gene: ENSMUSG00000028619
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Med26
|
60 |
111 |
7.9e-20 |
PFAM |
|
Pfam:TFIIS_M
|
126 |
207 |
1.7e-8 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000058585
|
| SMART Domains |
Protein: ENSMUSP00000054142
Gene: ENSMUSG00000028619
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Med26
|
61 |
110 |
5.5e-15 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000106753
AA Change: L16I
PolyPhen 2
Score 0.062 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000102364
Gene: ENSMUSG00000028618
AA Change: L16I
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:BSMAP
|
32 |
189 |
2.3e-43 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000127652
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000127720
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000128123
|
| SMART Domains |
Protein: ENSMUSP00000120288
Gene: ENSMUSG00000028618
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:BSMAP
|
18 |
127 |
1.7e-62 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129220
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000131474
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000132526
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000154007
AA Change: L16I
PolyPhen 2
Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000119701
Gene: ENSMUSG00000028618
AA Change: L16I
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
34 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147375
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141013
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000141165
|
| SMART Domains |
Protein: ENSMUSP00000115005
Gene: ENSMUSG00000028619
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Med26
|
60 |
111 |
1.1e-19 |
PFAM |
|
| Meta Mutation Damage Score |
0.0660 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.2%
- 20x: 94.7%
|
| Validation Efficiency |
100% (55/55) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein shown to regulate autophagy in response to bacterial infection. This protein may also regulate the retention of amyloid precursor protein (APP) in the Golgi apparatus through its control of APP glycosylation. Overexpression of this protein has been found to promote apoptosis in a glioma cell line. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]
PHENOTYPE: Mice homozygous for a null allele display reduced dendritic arborization, reduced miniature excitatory postsynaptic currents, and impaired memory formation. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2310003L06Rik |
A |
T |
5: 87,971,933 (GRCm38) |
D183V |
probably damaging |
Het |
| Ambra1 |
T |
A |
2: 91,885,719 (GRCm38) |
D858E |
probably damaging |
Het |
| Amdhd2 |
T |
C |
17: 24,156,604 (GRCm38) |
T370A |
probably benign |
Het |
| Amy1 |
A |
G |
3: 113,558,094 (GRCm38) |
W449R |
probably benign |
Het |
| Aox3 |
A |
T |
1: 58,186,280 (GRCm38) |
I1179F |
probably benign |
Het |
| Atp10a |
C |
A |
7: 58,824,327 (GRCm38) |
Q1121K |
probably damaging |
Het |
| Btaf1 |
C |
T |
19: 36,951,148 (GRCm38) |
A123V |
probably benign |
Het |
| Car6 |
T |
C |
4: 150,198,141 (GRCm38) |
K16E |
probably benign |
Het |
| Cgnl1 |
C |
T |
9: 71,656,096 (GRCm38) |
D779N |
probably benign |
Het |
| Cyp2a4 |
G |
A |
7: 26,308,537 (GRCm38) |
R123Q |
possibly damaging |
Het |
| D430041D05Rik |
C |
T |
2: 104,156,816 (GRCm38) |
R1895Q |
probably damaging |
Het |
| D5Ertd579e |
T |
A |
5: 36,616,206 (GRCm38) |
T282S |
probably benign |
Het |
| Dsel |
T |
C |
1: 111,859,962 (GRCm38) |
T948A |
probably benign |
Het |
| Ednrb |
A |
T |
14: 103,843,100 (GRCm38) |
I126N |
probably damaging |
Het |
| Egln1 |
A |
G |
8: 124,948,306 (GRCm38) |
M250T |
probably benign |
Het |
| Epb41l3 |
A |
T |
17: 69,253,468 (GRCm38) |
I337L |
possibly damaging |
Het |
| Epg5 |
T |
C |
18: 77,948,745 (GRCm38) |
I219T |
probably benign |
Het |
| Gm13030 |
T |
C |
4: 138,873,419 (GRCm38) |
|
probably benign |
Het |
| Gm1527 |
T |
A |
3: 28,926,661 (GRCm38) |
C637S |
probably benign |
Het |
| Hist1h1a |
A |
G |
13: 23,763,949 (GRCm38) |
N78S |
possibly damaging |
Het |
| Insrr |
T |
C |
3: 87,814,291 (GRCm38) |
I1168T |
possibly damaging |
Het |
| Ireb2 |
T |
C |
9: 54,896,552 (GRCm38) |
V509A |
possibly damaging |
Het |
| Kmt2c |
T |
C |
5: 25,354,717 (GRCm38) |
D981G |
probably damaging |
Het |
| Ktn1 |
A |
G |
14: 47,725,960 (GRCm38) |
E1164G |
probably damaging |
Het |
| L3hypdh |
A |
T |
12: 72,079,527 (GRCm38) |
V213E |
probably damaging |
Het |
| Masp1 |
T |
G |
16: 23,491,959 (GRCm38) |
D241A |
probably damaging |
Het |
| Mfsd13b |
A |
G |
7: 120,991,824 (GRCm38) |
I1V |
probably null |
Het |
| Muc5b |
T |
C |
7: 141,869,754 (GRCm38) |
V4531A |
probably benign |
Het |
| Myh2 |
A |
T |
11: 67,174,941 (GRCm38) |
|
probably null |
Het |
| Naip5 |
A |
G |
13: 100,221,533 (GRCm38) |
L1065P |
probably damaging |
Het |
| Necab1 |
T |
C |
4: 15,140,219 (GRCm38) |
|
probably benign |
Het |
| Nemf |
A |
G |
12: 69,353,786 (GRCm38) |
|
probably benign |
Het |
| Nfil3 |
A |
T |
13: 52,968,033 (GRCm38) |
D278E |
possibly damaging |
Het |
| Nup98 |
T |
C |
7: 102,180,424 (GRCm38) |
N393S |
probably damaging |
Het |
| Ogdh |
T |
A |
11: 6,349,393 (GRCm38) |
M753K |
probably benign |
Het |
| Olfr11 |
A |
T |
13: 21,639,436 (GRCm38) |
V29E |
probably damaging |
Het |
| Olfr1297 |
C |
T |
2: 111,621,739 (GRCm38) |
V112M |
probably benign |
Het |
| Olfr273 |
T |
C |
4: 52,855,568 (GRCm38) |
Y315C |
probably benign |
Het |
| Olfr561 |
T |
C |
7: 102,775,243 (GRCm38) |
F240L |
probably benign |
Het |
| Olfr901 |
T |
A |
9: 38,431,082 (GRCm38) |
S267T |
probably benign |
Het |
| Pkd2 |
A |
G |
5: 104,477,123 (GRCm38) |
K262E |
probably benign |
Het |
| Plce1 |
C |
T |
19: 38,727,013 (GRCm38) |
|
probably benign |
Het |
| Ppm1f |
T |
A |
16: 16,923,880 (GRCm38) |
M406K |
possibly damaging |
Het |
| Ptgs1 |
C |
T |
2: 36,242,847 (GRCm38) |
Q286* |
probably null |
Het |
| Scube2 |
T |
C |
7: 109,808,505 (GRCm38) |
T743A |
possibly damaging |
Het |
| Tipin |
T |
A |
9: 64,290,376 (GRCm38) |
L69* |
probably null |
Het |
| Tlk1 |
T |
A |
2: 70,738,445 (GRCm38) |
K404N |
probably damaging |
Het |
| Utrn |
T |
C |
10: 12,737,082 (GRCm38) |
E426G |
probably benign |
Het |
| Xdh |
A |
T |
17: 73,909,325 (GRCm38) |
S709T |
probably damaging |
Het |
| Yjefn3 |
T |
C |
8: 69,889,487 (GRCm38) |
N28D |
probably damaging |
Het |
| Zfp598 |
A |
C |
17: 24,679,667 (GRCm38) |
D480A |
probably damaging |
Het |
|
| Other mutations in Tmem59 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02663:Tmem59
|
APN |
4 |
107,197,541 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL02695:Tmem59
|
APN |
4 |
107,193,314 (GRCm38) |
missense |
probably benign |
0.00 |
|
IGL02699:Tmem59
|
APN |
4 |
107,192,538 (GRCm38) |
missense |
probably benign |
0.01 |
|
IGL02937:Tmem59
|
APN |
4 |
107,197,585 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0945:Tmem59
|
UTSW |
4 |
107,187,725 (GRCm38) |
splice site |
probably benign |
|
|
R4621:Tmem59
|
UTSW |
4 |
107,190,718 (GRCm38) |
intron |
probably benign |
|
|
R4622:Tmem59
|
UTSW |
4 |
107,190,718 (GRCm38) |
intron |
probably benign |
|
|
R4623:Tmem59
|
UTSW |
4 |
107,190,718 (GRCm38) |
intron |
probably benign |
|
|
R4819:Tmem59
|
UTSW |
4 |
107,187,681 (GRCm38) |
nonsense |
probably null |
|
|
R5413:Tmem59
|
UTSW |
4 |
107,200,462 (GRCm38) |
missense |
probably benign |
0.00 |
|
R5866:Tmem59
|
UTSW |
4 |
107,190,557 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R6073:Tmem59
|
UTSW |
4 |
107,193,401 (GRCm38) |
splice site |
probably null |
|
|
R8534:Tmem59
|
UTSW |
4 |
107,185,885 (GRCm38) |
critical splice donor site |
probably null |
|
|
R9727:Tmem59
|
UTSW |
4 |
107,193,350 (GRCm38) |
missense |
probably benign |
0.01 |
|
RF031:Tmem59
|
UTSW |
4 |
107,190,532 (GRCm38) |
critical splice acceptor site |
probably benign |
|
|
RF033:Tmem59
|
UTSW |
4 |
107,190,528 (GRCm38) |
critical splice acceptor site |
probably benign |
|
|
RF035:Tmem59
|
UTSW |
4 |
107,190,532 (GRCm38) |
critical splice acceptor site |
probably benign |
|
|
RF040:Tmem59
|
UTSW |
4 |
107,190,526 (GRCm38) |
critical splice acceptor site |
probably benign |
|
|
RF041:Tmem59
|
UTSW |
4 |
107,190,532 (GRCm38) |
critical splice acceptor site |
probably benign |
|
|
RF044:Tmem59
|
UTSW |
4 |
107,190,532 (GRCm38) |
critical splice acceptor site |
probably benign |
|
|
RF060:Tmem59
|
UTSW |
4 |
107,190,526 (GRCm38) |
critical splice acceptor site |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- AGAGGTTTTCCGTCCCAGAGAC -3'
(R):5'- GCACAAACTTCCGGCAATTTC -3'
Sequencing Primer
(F):5'- CAGGAGGCAGCCGATTG -3'
(R):5'- GCACAGCTTCACCACTAGGG -3'
|
| Posted On |
2014-09-17 |
Incidental Mutation