Incidental Mutation 'R5039:Tnfrsf1a'
| ID |
450620 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tnfrsf1a
|
| Ensembl Gene |
ENSMUSG00000030341 |
| Gene Name |
tumor necrosis factor receptor superfamily, member 1a |
| Synonyms |
TNFR60, TNFAR, TNF-R-I, TNFRp55, Tnfr1, TNF-alphaR1, CD120a, TNFalpha-R1, TNFRI, TNF receptor alpha chain, p55, TNF-alpha-R1, p55-R, TNF-R1, TNF-R55 |
| MMRRC Submission |
042629-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5039 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
125326686-125339446 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 125337675 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 89
(T89A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000117470
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000032491]
[ENSMUST00000042647]
[ENSMUST00000130257]
[ENSMUST00000144524]
|
| AlphaFold |
P25118 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000032491
AA Change: T211A
PolyPhen 2
Score 0.209 (Sensitivity: 0.92; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000032491
Gene: ENSMUSG00000030341
AA Change: T211A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
29 |
N/A |
INTRINSIC |
|
TNFR
|
44 |
81 |
2.4e-7 |
SMART |
|
TNFR
|
84 |
125 |
2.19e-10 |
SMART |
|
TNFR
|
127 |
166 |
5.43e-6 |
SMART |
|
TNFR
|
168 |
195 |
3.41e1 |
SMART |
|
transmembrane domain
|
212 |
234 |
N/A |
INTRINSIC |
|
low complexity region
|
263 |
276 |
N/A |
INTRINSIC |
|
low complexity region
|
290 |
301 |
N/A |
INTRINSIC |
|
DEATH
|
345 |
441 |
8.04e-18 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000042647
|
| SMART Domains |
Protein: ENSMUSP00000037004
Gene: ENSMUSG00000038167
| Domain | Start | End | E-Value | Type |
|---|
|
RhoGEF
|
165 |
352 |
1.5e-44 |
SMART |
|
PH
|
410 |
511 |
8.99e-7 |
SMART |
|
low complexity region
|
535 |
557 |
N/A |
INTRINSIC |
|
low complexity region
|
627 |
648 |
N/A |
INTRINSIC |
|
low complexity region
|
719 |
731 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000125880
|
| SMART Domains |
Protein: ENSMUSP00000121968
Gene: ENSMUSG00000030341
| Domain | Start | End | E-Value | Type |
|---|
|
TNFR
|
2 |
42 |
2.09e-7 |
SMART |
|
TNFR
|
44 |
83 |
5.43e-6 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000130257
|
| SMART Domains |
Protein: ENSMUSP00000115991
Gene: ENSMUSG00000030341
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
29 |
N/A |
INTRINSIC |
|
Pfam:TNFR_c6
|
44 |
66 |
1.1e-7 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000134803
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000144524
AA Change: T89A
PolyPhen 2
Score 0.670 (Sensitivity: 0.86; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000117470
Gene: ENSMUSG00000030341
AA Change: T89A
| Domain | Start | End | E-Value | Type |
|---|
|
TNFR
|
5 |
44 |
5.43e-6 |
SMART |
|
TNFR
|
46 |
73 |
3.41e1 |
SMART |
|
transmembrane domain
|
90 |
112 |
N/A |
INTRINSIC |
|
low complexity region
|
141 |
154 |
N/A |
INTRINSIC |
|
low complexity region
|
168 |
179 |
N/A |
INTRINSIC |
|
Blast:DEATH
|
223 |
295 |
1e-13 |
BLAST |
|
SCOP:d1icha_
|
269 |
295 |
3e-8 |
SMART |
|
| Meta Mutation Damage Score |
0.3756 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.5%
|
| Validation Efficiency |
100% (61/61) |
| MGI Phenotype |
FUNCTION: This gene encodes a member of the TNF receptor superfamily of proteins. The encoded receptor is found in membrane-bound and soluble forms that interact with membrane-bound and soluble forms, respectively, of its ligand, tumor necrosis factor alpha. Binding of membrane-bound tumor necrosis factor alpha to the membrane-bound receptor induces receptor trimerization and activation, which plays a role in cell survival, apoptosis, and inflammation. Proteolytic processing of the encoded receptor results in release of the soluble form of the receptor, which can interact with free tumor necrosis factor alpha to inhibit inflammation. Mice lacking a functional copy of this gene exhibit impaired immune function. [provided by RefSeq, Sep 2016]
PHENOTYPE: Homozygotes for targeted null mutations exhibit disrupted splenic architecture, increased adult liver weights, reduced IgG immune response, deficits in some host defense and inflammatory responses, LPS resistance, and reduced graft-vs-host disease. [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 |
|---|
| Abcg4 |
G |
A |
9: 44,192,863 (GRCm39) |
A161V |
probably damaging |
Het |
| Anapc2 |
T |
C |
2: 25,164,808 (GRCm39) |
I64T |
possibly damaging |
Het |
| Arfgef1 |
T |
C |
1: 10,269,961 (GRCm39) |
D396G |
probably benign |
Het |
| Ark2c |
A |
G |
18: 77,550,608 (GRCm39) |
S107P |
probably damaging |
Het |
| Axl |
C |
T |
7: 25,485,340 (GRCm39) |
V163M |
probably damaging |
Het |
| Blm |
G |
A |
7: 80,155,621 (GRCm39) |
P353S |
possibly damaging |
Het |
| Btaf1 |
T |
C |
19: 36,968,162 (GRCm39) |
Y1116H |
probably benign |
Het |
| Ccdc18 |
T |
A |
5: 108,306,514 (GRCm39) |
|
probably null |
Het |
| Ccdc87 |
T |
C |
19: 4,890,429 (GRCm39) |
|
probably null |
Het |
| Cdhr1 |
T |
C |
14: 36,801,600 (GRCm39) |
N781S |
probably benign |
Het |
| Ctr9 |
C |
A |
7: 110,642,064 (GRCm39) |
H297Q |
probably benign |
Het |
| Cyp2c55 |
A |
G |
19: 39,026,587 (GRCm39) |
D398G |
probably benign |
Het |
| Dnase1l1 |
C |
T |
X: 73,320,644 (GRCm39) |
|
probably null |
Het |
| Dnmt3l |
T |
C |
10: 77,888,734 (GRCm39) |
|
probably null |
Het |
| Dock4 |
C |
A |
12: 40,867,745 (GRCm39) |
N1440K |
probably damaging |
Het |
| Etnk1 |
T |
A |
6: 143,141,043 (GRCm39) |
|
probably null |
Het |
| Fam120a |
A |
T |
13: 49,063,726 (GRCm39) |
|
probably null |
Het |
| Fanca |
T |
C |
8: 124,010,785 (GRCm39) |
D908G |
probably benign |
Het |
| Gm17535 |
T |
A |
9: 3,035,786 (GRCm39) |
L218H |
probably benign |
Het |
| Gm3633 |
A |
C |
14: 42,461,161 (GRCm39) |
N42K |
possibly damaging |
Het |
| Gm4781 |
C |
A |
10: 100,232,851 (GRCm39) |
|
noncoding transcript |
Het |
| Gm8741 |
G |
T |
17: 35,555,062 (GRCm39) |
|
noncoding transcript |
Het |
| Gpr139 |
A |
G |
7: 118,744,165 (GRCm39) |
V140A |
probably benign |
Het |
| Ighv1-62-3 |
G |
T |
12: 115,425,014 (GRCm39) |
T13K |
probably benign |
Het |
| Itgb2l |
T |
C |
16: 96,226,205 (GRCm39) |
T629A |
possibly damaging |
Het |
| Kcnb2 |
T |
C |
1: 15,779,724 (GRCm39) |
S199P |
probably damaging |
Het |
| Kdm1b |
G |
A |
13: 47,230,962 (GRCm39) |
G663D |
probably damaging |
Het |
| Lama1 |
A |
G |
17: 68,052,888 (GRCm39) |
D407G |
possibly damaging |
Het |
| Macf1 |
T |
C |
4: 123,405,013 (GRCm39) |
K391R |
probably damaging |
Het |
| Magi3 |
A |
T |
3: 104,013,107 (GRCm39) |
S127T |
probably damaging |
Het |
| Map2 |
A |
T |
1: 66,477,955 (GRCm39) |
D1759V |
probably damaging |
Het |
| Mllt6 |
G |
A |
11: 97,560,326 (GRCm39) |
S210N |
possibly damaging |
Het |
| Myrfl |
T |
C |
10: 116,658,616 (GRCm39) |
D447G |
probably damaging |
Het |
| Ndufb7 |
A |
G |
8: 84,298,094 (GRCm39) |
|
probably benign |
Het |
| Nt5e |
T |
A |
9: 88,245,634 (GRCm39) |
N301K |
probably benign |
Het |
| Or10d4b |
A |
T |
9: 39,534,856 (GRCm39) |
T146S |
possibly damaging |
Het |
| Or8g27 |
T |
A |
9: 39,129,410 (GRCm39) |
Y252* |
probably null |
Het |
| Pcdh10 |
A |
G |
3: 45,336,296 (GRCm39) |
N870S |
probably damaging |
Het |
| Pcdh18 |
A |
G |
3: 49,709,305 (GRCm39) |
V670A |
probably benign |
Het |
| Phf8-ps |
A |
C |
17: 33,286,734 (GRCm39) |
C23G |
probably damaging |
Het |
| Polr1c |
G |
T |
17: 46,558,635 (GRCm39) |
|
probably benign |
Het |
| Ric3 |
G |
C |
7: 108,637,930 (GRCm39) |
S274R |
probably benign |
Het |
| Rimbp3 |
A |
G |
16: 17,031,195 (GRCm39) |
T1540A |
probably damaging |
Het |
| Rp1l1 |
A |
T |
14: 64,268,805 (GRCm39) |
M1464L |
probably benign |
Het |
| Slc41a3 |
A |
G |
6: 90,603,399 (GRCm39) |
Y140C |
probably damaging |
Het |
| Ssb |
A |
T |
2: 69,696,581 (GRCm39) |
E38D |
possibly damaging |
Het |
| Syt14 |
A |
T |
1: 192,709,292 (GRCm39) |
I16N |
probably damaging |
Het |
| Tet3 |
T |
C |
6: 83,352,878 (GRCm39) |
T973A |
probably damaging |
Het |
| Tial1 |
T |
C |
7: 128,045,692 (GRCm39) |
|
probably benign |
Het |
| Trpv5 |
T |
C |
6: 41,652,879 (GRCm39) |
Y98C |
possibly damaging |
Het |
| Ylpm1 |
T |
A |
12: 85,062,267 (GRCm39) |
S265T |
probably damaging |
Het |
| Ylpm1 |
A |
G |
12: 85,089,013 (GRCm39) |
D1006G |
probably damaging |
Het |
|
| Other mutations in Tnfrsf1a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01987:Tnfrsf1a
|
APN |
6 |
125,333,827 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02468:Tnfrsf1a
|
APN |
6 |
125,334,824 (GRCm39) |
missense |
probably benign |
0.06 |
|
IGL02588:Tnfrsf1a
|
APN |
6 |
125,337,729 (GRCm39) |
missense |
probably benign |
0.44 |
|
R1302:Tnfrsf1a
|
UTSW |
6 |
125,333,879 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2189:Tnfrsf1a
|
UTSW |
6 |
125,334,768 (GRCm39) |
missense |
probably benign |
0.42 |
|
R4559:Tnfrsf1a
|
UTSW |
6 |
125,337,729 (GRCm39) |
missense |
probably benign |
0.44 |
|
R4794:Tnfrsf1a
|
UTSW |
6 |
125,335,047 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5364:Tnfrsf1a
|
UTSW |
6 |
125,334,356 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R5792:Tnfrsf1a
|
UTSW |
6 |
125,335,040 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6742:Tnfrsf1a
|
UTSW |
6 |
125,333,911 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7018:Tnfrsf1a
|
UTSW |
6 |
125,333,914 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7128:Tnfrsf1a
|
UTSW |
6 |
125,338,499 (GRCm39) |
missense |
probably benign |
0.11 |
|
R7192:Tnfrsf1a
|
UTSW |
6 |
125,338,559 (GRCm39) |
missense |
unknown |
|
|
R7715:Tnfrsf1a
|
UTSW |
6 |
125,338,377 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R8745:Tnfrsf1a
|
UTSW |
6 |
125,338,745 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8755:Tnfrsf1a
|
UTSW |
6 |
125,334,768 (GRCm39) |
missense |
probably benign |
0.42 |
|
R8856:Tnfrsf1a
|
UTSW |
6 |
125,334,688 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R9005:Tnfrsf1a
|
UTSW |
6 |
125,333,878 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- ACCTCCTCCGCTTGCAAATG -3'
(R):5'- AGCCTAGAGTCCTTAACCATGAAG -3'
Sequencing Primer
(F):5'- TCCGCTTGCAAATGTCACAAAC -3'
(R):5'- GTCCTTAACCATGAAGAGAGGCC -3'
|
| Posted On |
2016-12-27 |
Incidental Mutation