Incidental Mutation 'R2397:Nr1h3'
| ID |
248540 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nr1h3
|
| Ensembl Gene |
ENSMUSG00000002108 |
| Gene Name |
nuclear receptor subfamily 1, group H, member 3 |
| Synonyms |
Unr1, LXR alpha |
| MMRRC Submission |
040364-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2397 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
91014406-91033179 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 91022202 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Isoleucine
at position 142
(T142I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000106988
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000002177]
[ENSMUST00000111354]
[ENSMUST00000111355]
[ENSMUST00000111356]
|
| AlphaFold |
Q9Z0Y9 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000002177
AA Change: T142I
PolyPhen 2
Score 0.810 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000002177
Gene: ENSMUSG00000002108
AA Change: T142I
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_C4
|
93 |
164 |
1e-35 |
SMART |
|
low complexity region
|
189 |
209 |
N/A |
INTRINSIC |
|
HOLI
|
257 |
416 |
1.84e-43 |
SMART |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000111354
AA Change: T142I
PolyPhen 2
Score 0.810 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000106986
Gene: ENSMUSG00000002108
AA Change: T142I
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_C4
|
93 |
164 |
1e-35 |
SMART |
|
low complexity region
|
189 |
209 |
N/A |
INTRINSIC |
|
HOLI
|
257 |
416 |
1.84e-43 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111355
AA Change: T142I
PolyPhen 2
Score 0.273 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000106987
Gene: ENSMUSG00000002108
AA Change: T142I
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_C4
|
93 |
164 |
1e-35 |
SMART |
|
HOLI
|
202 |
356 |
3.76e-17 |
SMART |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000111356
AA Change: T142I
PolyPhen 2
Score 0.810 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000106988
Gene: ENSMUSG00000002108
AA Change: T142I
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_C4
|
93 |
164 |
1e-35 |
SMART |
|
low complexity region
|
189 |
209 |
N/A |
INTRINSIC |
|
HOLI
|
257 |
416 |
1.84e-43 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130031
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000131634
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000133261
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150654
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000136234
|
| Meta Mutation Damage Score |
0.0950 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.4%
- 10x: 96.8%
- 20x: 93.4%
|
| Validation Efficiency |
98% (41/42) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the NR1 subfamily of the nuclear receptor superfamily. The NR1 family members are key regulators of macrophage function, controlling transcriptional programs involved in lipid homeostasis and inflammation. This protein is highly expressed in visceral organs, including liver, kidney and intestine. It forms a heterodimer with retinoid X receptor (RXR), and regulates expression of target genes containing retinoid response elements. Studies in mice lacking this gene suggest that it may play an important role in the regulation of cholesterol homeostasis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit decreased male fertility, increased suseceptibility to bacterial infection, and diet-sensitive increase in liver size, steatosis, and cholesterol level. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 41 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam29 |
T |
A |
8: 56,325,933 (GRCm39) |
M174L |
probably benign |
Het |
| Adamtsl1 |
C |
T |
4: 86,117,594 (GRCm39) |
R186W |
probably damaging |
Het |
| Agtpbp1 |
C |
T |
13: 59,622,383 (GRCm39) |
V948I |
probably benign |
Het |
| Atp13a2 |
A |
G |
4: 140,730,466 (GRCm39) |
T787A |
probably benign |
Het |
| Capn11 |
T |
A |
17: 45,964,147 (GRCm39) |
N139I |
probably damaging |
Het |
| Cars1 |
T |
C |
7: 143,146,244 (GRCm39) |
D60G |
possibly damaging |
Het |
| Cers1 |
A |
T |
8: 70,774,186 (GRCm39) |
I148F |
probably benign |
Het |
| Col14a1 |
T |
C |
15: 55,201,835 (GRCm39) |
I41T |
unknown |
Het |
| Cyp2d26 |
C |
T |
15: 82,678,236 (GRCm39) |
G47R |
probably damaging |
Het |
| Dhx36 |
A |
T |
3: 62,405,518 (GRCm39) |
M205K |
probably benign |
Het |
| Dyrk2 |
T |
A |
10: 118,697,273 (GRCm39) |
|
probably benign |
Het |
| Echs1 |
T |
C |
7: 139,692,390 (GRCm39) |
H119R |
possibly damaging |
Het |
| Ehf |
T |
A |
2: 103,107,164 (GRCm39) |
D120V |
probably damaging |
Het |
| Esrra |
A |
G |
19: 6,897,544 (GRCm39) |
L71P |
probably damaging |
Het |
| Fam228a |
A |
T |
12: 4,768,718 (GRCm39) |
S200R |
probably benign |
Het |
| Fibcd1 |
A |
T |
2: 31,724,435 (GRCm39) |
M191K |
probably benign |
Het |
| Foxn4 |
A |
G |
5: 114,393,556 (GRCm39) |
L521P |
probably damaging |
Het |
| Fscn2 |
T |
C |
11: 120,252,995 (GRCm39) |
L154P |
probably damaging |
Het |
| Gm7964 |
T |
G |
7: 83,406,321 (GRCm39) |
|
noncoding transcript |
Het |
| Golga3 |
T |
C |
5: 110,353,743 (GRCm39) |
|
probably benign |
Het |
| Gria4 |
A |
G |
9: 4,537,717 (GRCm39) |
L197P |
probably damaging |
Het |
| Heg1 |
T |
A |
16: 33,562,849 (GRCm39) |
M913K |
probably damaging |
Het |
| Ifi205 |
T |
C |
1: 173,845,141 (GRCm39) |
T214A |
possibly damaging |
Het |
| Ift140 |
T |
G |
17: 25,239,710 (GRCm39) |
D122E |
probably damaging |
Het |
| Jakmip1 |
T |
A |
5: 37,258,087 (GRCm39) |
D244E |
probably damaging |
Het |
| Krt84 |
A |
G |
15: 101,438,689 (GRCm39) |
V266A |
probably benign |
Het |
| Mc2r |
T |
A |
18: 68,541,224 (GRCm39) |
D23V |
probably benign |
Het |
| Ncr1 |
T |
A |
7: 4,341,260 (GRCm39) |
F47I |
probably benign |
Het |
| Obox2 |
C |
T |
7: 15,130,971 (GRCm39) |
P68S |
probably benign |
Het |
| Pacs2 |
G |
A |
12: 113,026,987 (GRCm39) |
D605N |
probably damaging |
Het |
| Parn |
A |
G |
16: 13,384,518 (GRCm39) |
V515A |
probably benign |
Het |
| Ptdss2 |
T |
A |
7: 140,727,005 (GRCm39) |
F105I |
probably benign |
Het |
| Ruvbl1 |
A |
C |
6: 88,442,534 (GRCm39) |
T9P |
possibly damaging |
Het |
| Slc15a3 |
A |
G |
19: 10,820,407 (GRCm39) |
E8G |
probably benign |
Het |
| Slf1 |
G |
T |
13: 77,251,702 (GRCm39) |
Y303* |
probably null |
Het |
| Socs5 |
T |
C |
17: 87,442,377 (GRCm39) |
F439S |
probably damaging |
Het |
| Tcp10c |
C |
A |
17: 13,590,473 (GRCm39) |
A357E |
probably damaging |
Het |
| Tmem200c |
T |
C |
17: 69,147,942 (GRCm39) |
V175A |
probably damaging |
Het |
| Vmn2r124 |
T |
A |
17: 18,269,859 (GRCm39) |
H38Q |
possibly damaging |
Het |
| Vmn2r54 |
T |
G |
7: 12,349,578 (GRCm39) |
Q668P |
probably damaging |
Het |
| Xrcc2 |
T |
C |
5: 25,910,708 (GRCm39) |
S3G |
probably null |
Het |
|
| Other mutations in Nr1h3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00496:Nr1h3
|
APN |
2 |
91,020,544 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02198:Nr1h3
|
APN |
2 |
91,023,070 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02992:Nr1h3
|
APN |
2 |
91,020,911 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03103:Nr1h3
|
APN |
2 |
91,022,360 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0302:Nr1h3
|
UTSW |
2 |
91,022,358 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R0350:Nr1h3
|
UTSW |
2 |
91,022,170 (GRCm39) |
missense |
possibly damaging |
0.68 |
|
R2439:Nr1h3
|
UTSW |
2 |
91,020,565 (GRCm39) |
missense |
probably benign |
0.45 |
|
R2988:Nr1h3
|
UTSW |
2 |
91,015,349 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R3431:Nr1h3
|
UTSW |
2 |
91,022,205 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4842:Nr1h3
|
UTSW |
2 |
91,020,563 (GRCm39) |
missense |
probably benign |
0.09 |
|
R5355:Nr1h3
|
UTSW |
2 |
91,022,253 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
R6137:Nr1h3
|
UTSW |
2 |
91,022,196 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6982:Nr1h3
|
UTSW |
2 |
91,021,104 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7380:Nr1h3
|
UTSW |
2 |
91,020,540 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R7531:Nr1h3
|
UTSW |
2 |
91,014,739 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7753:Nr1h3
|
UTSW |
2 |
91,015,370 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7980:Nr1h3
|
UTSW |
2 |
91,021,229 (GRCm39) |
missense |
probably benign |
0.03 |
|
R8831:Nr1h3
|
UTSW |
2 |
91,021,091 (GRCm39) |
missense |
probably benign |
0.27 |
|
R8861:Nr1h3
|
UTSW |
2 |
91,024,026 (GRCm39) |
start gained |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GGAAGTTTTAATCCACACTCAGG -3'
(R):5'- TGTGTCTCTATCCAGAGCTTCG -3'
Sequencing Primer
(F):5'- CACTCAGGAGATCTCTGCAAGTG -3'
(R):5'- GAGCTTCGTCCACAAAAGCGG -3'
|
| Posted On |
2014-11-11 |
Incidental Mutation