Incidental Mutation 'R4996:Rfx5'
| ID |
385235 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rfx5
|
| Ensembl Gene |
ENSMUSG00000005774 |
| Gene Name |
regulatory factor X, 5 (influences HLA class II expression) |
| Synonyms |
|
| MMRRC Submission |
042590-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.242)
|
| Stock # |
R4996 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
94861355-94868685 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 94863126 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Isoleucine
at position 73
(V73I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000117963
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029772]
[ENSMUST00000107253]
[ENSMUST00000107254]
[ENSMUST00000107255]
[ENSMUST00000107260]
[ENSMUST00000132393]
[ENSMUST00000137088]
[ENSMUST00000145031]
[ENSMUST00000147237]
[ENSMUST00000152869]
[ENSMUST00000142311]
[ENSMUST00000140331]
[ENSMUST00000144132]
[ENSMUST00000145472]
|
| AlphaFold |
Q9JL61 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029772
AA Change: V73I
PolyPhen 2
Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
AA Change: V73I
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX_DNA_binding
|
84 |
169 |
7.2e-33 |
PFAM |
|
RFX5_DNA_bdg
|
438 |
656 |
4.29e-130 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000107253
AA Change: V73I
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000102874
Gene: ENSMUSG00000005774
AA Change: V73I
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX_DNA_binding
|
84 |
169 |
1.8e-33 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000107254
AA Change: V73I
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000102875
Gene: ENSMUSG00000005774
AA Change: V73I
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX_DNA_binding
|
84 |
169 |
1.8e-33 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000107255
AA Change: V73I
PolyPhen 2
Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
AA Change: V73I
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX_DNA_binding
|
84 |
169 |
7.2e-33 |
PFAM |
|
RFX5_DNA_bdg
|
438 |
656 |
4.29e-130 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000107260
AA Change: V73I
PolyPhen 2
Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
AA Change: V73I
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX_DNA_binding
|
88 |
167 |
5.3e-31 |
PFAM |
|
RFX5_DNA_bdg
|
438 |
656 |
4.29e-130 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000125186
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000132393
AA Change: V73I
PolyPhen 2
Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000117999
Gene: ENSMUSG00000005774
AA Change: V73I
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:2KW3|B
|
23 |
89 |
9e-40 |
PDB |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000137088
AA Change: V73I
PolyPhen 2
Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
AA Change: V73I
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX_DNA_binding
|
84 |
169 |
7.2e-33 |
PFAM |
|
RFX5_DNA_bdg
|
438 |
656 |
4.29e-130 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000145031
AA Change: V73I
PolyPhen 2
Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000118099
Gene: ENSMUSG00000005774
AA Change: V73I
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:2KW3|B
|
23 |
89 |
9e-40 |
PDB |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000147237
AA Change: V73I
PolyPhen 2
Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000118586
Gene: ENSMUSG00000005774
AA Change: V73I
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX_DNA_binding
|
84 |
169 |
8.7e-34 |
PFAM |
|
Pfam:Pox_D5
|
88 |
159 |
1e-7 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148803
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000152869
AA Change: V73I
PolyPhen 2
Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000121157
Gene: ENSMUSG00000005774
AA Change: V73I
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:2KW3|B
|
23 |
89 |
7e-40 |
PDB |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000142311
AA Change: V73I
PolyPhen 2
Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000119704
Gene: ENSMUSG00000005774
AA Change: V73I
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX_DNA_binding
|
84 |
131 |
4.1e-10 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140294
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000142708
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000140331
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000144132
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000145472
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.1%
- 20x: 91.5%
|
| Validation Efficiency |
|
| MGI Phenotype |
PHENOTYPE: Homozygous null mice have absent or decreased expression of MHC-II complexes on antigen presenting cells, which leads to reduced numbers of CD4+ thymocytes and T cells. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 77 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930505A04Rik |
C |
T |
11: 30,376,349 (GRCm39) |
V173M |
probably damaging |
Het |
| Actl11 |
A |
G |
9: 107,808,934 (GRCm39) |
I1086V |
possibly damaging |
Het |
| Adgrv1 |
T |
C |
13: 81,726,853 (GRCm39) |
S500G |
probably benign |
Het |
| Ahcyl1 |
A |
T |
3: 107,575,603 (GRCm39) |
V394E |
probably damaging |
Het |
| Alg9 |
T |
C |
9: 50,720,005 (GRCm39) |
F494L |
probably damaging |
Het |
| Ankrd55 |
C |
A |
13: 112,492,622 (GRCm39) |
D264E |
possibly damaging |
Het |
| Asb14 |
A |
G |
14: 26,634,073 (GRCm39) |
N426S |
possibly damaging |
Het |
| Atm |
A |
T |
9: 53,435,807 (GRCm39) |
F168I |
probably benign |
Het |
| Atp13a4 |
A |
T |
16: 29,290,822 (GRCm39) |
I209N |
probably damaging |
Het |
| BB014433 |
A |
T |
8: 15,092,166 (GRCm39) |
L229Q |
probably benign |
Het |
| Calml3 |
T |
C |
13: 3,854,142 (GRCm39) |
D21G |
probably damaging |
Het |
| Capn10 |
A |
G |
1: 92,872,858 (GRCm39) |
N528S |
probably damaging |
Het |
| Ccnl2 |
T |
A |
4: 155,897,981 (GRCm39) |
D141E |
possibly damaging |
Het |
| Cd163 |
A |
G |
6: 124,296,106 (GRCm39) |
I817V |
probably benign |
Het |
| Cgnl1 |
CTTGCCCAGGTT |
CTT |
9: 71,632,108 (GRCm39) |
|
probably benign |
Het |
| Cln6 |
T |
A |
9: 62,757,937 (GRCm39) |
I232N |
probably damaging |
Het |
| Col22a1 |
A |
C |
15: 71,879,010 (GRCm39) |
V49G |
probably damaging |
Het |
| Csmd1 |
A |
T |
8: 15,960,452 (GRCm39) |
M3321K |
probably damaging |
Het |
| Cyp2u1 |
T |
A |
3: 131,091,933 (GRCm39) |
M196L |
probably benign |
Het |
| Dlec1 |
T |
G |
9: 118,975,118 (GRCm39) |
L1566R |
probably damaging |
Het |
| Dnajc3 |
A |
G |
14: 119,209,839 (GRCm39) |
T305A |
probably benign |
Het |
| Drp2 |
G |
A |
X: 133,342,065 (GRCm39) |
R567H |
probably damaging |
Homo |
| Efhd1 |
G |
T |
1: 87,192,280 (GRCm39) |
G37W |
possibly damaging |
Het |
| Exph5 |
G |
C |
9: 53,286,910 (GRCm39) |
E1330D |
possibly damaging |
Het |
| Fbln2 |
A |
T |
6: 91,242,992 (GRCm39) |
Y913F |
probably benign |
Het |
| Fmnl1 |
G |
A |
11: 103,073,482 (GRCm39) |
S167N |
possibly damaging |
Het |
| Frs3 |
A |
G |
17: 48,012,635 (GRCm39) |
E114G |
probably damaging |
Het |
| Gmpr2 |
T |
C |
14: 55,914,252 (GRCm39) |
I169T |
probably damaging |
Het |
| Gria2 |
A |
G |
3: 80,614,448 (GRCm39) |
S531P |
probably damaging |
Het |
| Hace1 |
G |
A |
10: 45,526,046 (GRCm39) |
A296T |
probably benign |
Het |
| Ift70a1 |
C |
T |
2: 75,810,266 (GRCm39) |
G606S |
probably benign |
Het |
| Inhbb |
A |
C |
1: 119,348,548 (GRCm39) |
L90R |
probably damaging |
Het |
| Insr |
C |
T |
8: 3,242,665 (GRCm39) |
R18Q |
probably null |
Het |
| Kdm6b |
G |
T |
11: 69,296,557 (GRCm39) |
P570Q |
probably damaging |
Het |
| Lama3 |
T |
C |
18: 12,651,800 (GRCm39) |
V1803A |
probably benign |
Het |
| Lpin3 |
T |
A |
2: 160,747,207 (GRCm39) |
L811Q |
probably damaging |
Het |
| Lrrc8e |
C |
T |
8: 4,285,166 (GRCm39) |
L464F |
probably damaging |
Het |
| Micall2 |
A |
G |
5: 139,696,344 (GRCm39) |
S729P |
probably benign |
Het |
| Naca |
C |
T |
10: 127,878,298 (GRCm39) |
|
probably benign |
Het |
| Nav1 |
A |
T |
1: 135,393,709 (GRCm39) |
S1010T |
probably damaging |
Het |
| Nefm |
T |
C |
14: 68,358,570 (GRCm39) |
|
probably benign |
Het |
| Nlrp9c |
A |
T |
7: 26,085,172 (GRCm39) |
F136I |
possibly damaging |
Het |
| Nup210 |
A |
T |
6: 91,030,418 (GRCm39) |
F137Y |
probably benign |
Het |
| Or1o3 |
A |
G |
17: 37,573,758 (GRCm39) |
S266P |
probably benign |
Het |
| Or3a1c |
A |
G |
11: 74,046,157 (GRCm39) |
H59R |
probably damaging |
Het |
| Or8k32 |
T |
C |
2: 86,368,615 (GRCm39) |
I215V |
probably benign |
Het |
| Otog |
C |
A |
7: 45,948,030 (GRCm39) |
H2344N |
possibly damaging |
Het |
| Otog |
C |
A |
7: 45,954,934 (GRCm39) |
C517* |
probably null |
Het |
| Pcdhac1 |
C |
T |
18: 37,225,580 (GRCm39) |
Q798* |
probably null |
Het |
| Pdhx |
T |
C |
2: 102,860,657 (GRCm39) |
D330G |
probably damaging |
Het |
| Peg10 |
ACATCAGGATCC |
ACATCAGGATCCCCATCAGGATCC |
6: 4,756,454 (GRCm39) |
|
probably benign |
Het |
| Pgr |
C |
A |
9: 8,900,914 (GRCm39) |
P149Q |
probably damaging |
Het |
| Plaat1 |
G |
A |
16: 29,036,456 (GRCm39) |
W31* |
probably null |
Het |
| Ppm1h |
A |
T |
10: 122,777,245 (GRCm39) |
I504F |
probably damaging |
Het |
| Ppp6r3 |
A |
G |
19: 3,523,833 (GRCm39) |
S556P |
probably damaging |
Het |
| Ranbp9 |
G |
A |
13: 43,578,570 (GRCm39) |
Q168* |
probably null |
Het |
| Relb |
A |
T |
7: 19,349,528 (GRCm39) |
L259Q |
probably benign |
Het |
| Rgcc |
T |
C |
14: 79,527,716 (GRCm39) |
D125G |
possibly damaging |
Het |
| Rmnd5b |
A |
G |
11: 51,518,735 (GRCm39) |
V86A |
probably damaging |
Het |
| Slc15a5 |
G |
A |
6: 138,020,583 (GRCm39) |
T250M |
probably damaging |
Het |
| Slc7a2 |
A |
T |
8: 41,365,599 (GRCm39) |
K477* |
probably null |
Het |
| Slx9 |
A |
T |
10: 77,351,367 (GRCm39) |
W14R |
probably null |
Het |
| Smc2 |
T |
A |
4: 52,461,042 (GRCm39) |
|
probably null |
Het |
| Sox5 |
A |
T |
6: 143,974,070 (GRCm39) |
L226* |
probably null |
Het |
| Sp140l2 |
G |
T |
1: 85,224,815 (GRCm39) |
A240E |
probably benign |
Het |
| Syne2 |
A |
G |
12: 75,990,724 (GRCm39) |
E1903G |
possibly damaging |
Het |
| Tenm3 |
A |
T |
8: 48,688,861 (GRCm39) |
I2226N |
probably damaging |
Het |
| Tmtc3 |
A |
T |
10: 100,283,086 (GRCm39) |
I823N |
probably damaging |
Het |
| Top6bl |
T |
A |
19: 4,676,112 (GRCm39) |
K673N |
probably benign |
Het |
| Tor3a |
T |
C |
1: 156,483,342 (GRCm39) |
Y360C |
probably damaging |
Het |
| Trpc3 |
T |
C |
3: 36,716,967 (GRCm39) |
E357G |
probably benign |
Het |
| Tubgcp6 |
A |
T |
15: 88,987,693 (GRCm39) |
N1093K |
possibly damaging |
Het |
| Vmn1r64 |
T |
A |
7: 5,887,052 (GRCm39) |
T164S |
probably benign |
Het |
| Vmn2r40 |
T |
A |
7: 8,911,166 (GRCm39) |
Q709L |
probably damaging |
Het |
| Vmn2r81 |
A |
T |
10: 79,129,247 (GRCm39) |
I713L |
probably benign |
Het |
| Washc5 |
T |
C |
15: 59,205,484 (GRCm39) |
T686A |
probably benign |
Het |
| Wipf1 |
GCCTCCTCCTCCTCCTCCTCCTCC |
GCCTCCTCCTCCTCCTCCTCC |
2: 73,270,418 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Rfx5 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01459:Rfx5
|
APN |
3 |
94,865,086 (GRCm39) |
unclassified |
probably benign |
|
|
IGL01478:Rfx5
|
APN |
3 |
94,865,751 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
IGL02061:Rfx5
|
APN |
3 |
94,865,792 (GRCm39) |
missense |
probably benign |
0.03 |
|
IGL02152:Rfx5
|
APN |
3 |
94,864,493 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03395:Rfx5
|
APN |
3 |
94,865,113 (GRCm39) |
nonsense |
probably null |
|
|
chip
|
UTSW |
3 |
94,863,666 (GRCm39) |
missense |
probably damaging |
1.00 |
|
nonplussed
|
UTSW |
3 |
94,866,272 (GRCm39) |
missense |
unknown |
|
|
shrunken
|
UTSW |
3 |
94,862,454 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0098:Rfx5
|
UTSW |
3 |
94,865,679 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0098:Rfx5
|
UTSW |
3 |
94,865,679 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0505:Rfx5
|
UTSW |
3 |
94,863,666 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0681:Rfx5
|
UTSW |
3 |
94,863,666 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1342:Rfx5
|
UTSW |
3 |
94,865,723 (GRCm39) |
missense |
probably benign |
0.09 |
|
R1460:Rfx5
|
UTSW |
3 |
94,863,636 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1466:Rfx5
|
UTSW |
3 |
94,863,614 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1466:Rfx5
|
UTSW |
3 |
94,863,614 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1972:Rfx5
|
UTSW |
3 |
94,864,603 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2173:Rfx5
|
UTSW |
3 |
94,864,027 (GRCm39) |
splice site |
probably null |
|
|
R4808:Rfx5
|
UTSW |
3 |
94,865,591 (GRCm39) |
missense |
probably benign |
0.03 |
|
R4993:Rfx5
|
UTSW |
3 |
94,863,126 (GRCm39) |
missense |
probably benign |
0.27 |
|
R5104:Rfx5
|
UTSW |
3 |
94,862,451 (GRCm39) |
missense |
probably benign |
0.35 |
|
R5912:Rfx5
|
UTSW |
3 |
94,866,029 (GRCm39) |
unclassified |
probably benign |
|
|
R7097:Rfx5
|
UTSW |
3 |
94,863,850 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7186:Rfx5
|
UTSW |
3 |
94,865,659 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7194:Rfx5
|
UTSW |
3 |
94,862,454 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7202:Rfx5
|
UTSW |
3 |
94,866,272 (GRCm39) |
missense |
unknown |
|
|
R7203:Rfx5
|
UTSW |
3 |
94,866,187 (GRCm39) |
missense |
unknown |
|
|
R7374:Rfx5
|
UTSW |
3 |
94,866,053 (GRCm39) |
missense |
unknown |
|
|
R7375:Rfx5
|
UTSW |
3 |
94,866,053 (GRCm39) |
missense |
unknown |
|
|
R8919:Rfx5
|
UTSW |
3 |
94,864,475 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9562:Rfx5
|
UTSW |
3 |
94,866,639 (GRCm39) |
missense |
unknown |
|
|
RF061:Rfx5
|
UTSW |
3 |
94,863,070 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Rfx5
|
UTSW |
3 |
94,863,126 (GRCm39) |
missense |
probably benign |
0.27 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTCTGACAACCTGACATCGAG -3'
(R):5'- GGTTCTGAGCTATGCATCTCCTAC -3'
Sequencing Primer
(F):5'- ACATCGAGTCAGCTGGTATG -3'
(R):5'- TGTCGGATTTCCAGAAACTGAG -3'
|
| Posted On |
2016-05-10 |
Incidental Mutation