Incidental Mutation 'R9359:Rfx4'
| ID |
708587 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rfx4
|
| Ensembl Gene |
ENSMUSG00000020037 |
| Gene Name |
regulatory factor X, 4 (influences HLA class II expression) |
| Synonyms |
4933412G19Rik |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R9359 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
84591926-84742402 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 84740921 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 680
(T680A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000051107
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000060397]
[ENSMUST00000095388]
[ENSMUST00000166696]
|
| AlphaFold |
Q7TNK1 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000060397
AA Change: T680A
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: T680A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX_DNA_binding
|
58 |
136 |
7.9e-37 |
PFAM |
|
Blast:HisKA
|
293 |
356 |
5e-7 |
BLAST |
|
low complexity region
|
503 |
515 |
N/A |
INTRINSIC |
|
low complexity region
|
521 |
537 |
N/A |
INTRINSIC |
|
low complexity region
|
599 |
611 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000095388
AA Change: T586A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: T586A
| Domain | Start | End | E-Value | Type |
|---|
|
SCOP:d1kwha_
|
11 |
201 |
6e-3 |
SMART |
|
Blast:HisKA
|
199 |
262 |
4e-7 |
BLAST |
|
low complexity region
|
409 |
421 |
N/A |
INTRINSIC |
|
low complexity region
|
427 |
443 |
N/A |
INTRINSIC |
|
low complexity region
|
505 |
517 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000166696
AA Change: T537A
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: T537A
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:HisKA
|
150 |
213 |
6e-7 |
BLAST |
|
low complexity region
|
360 |
372 |
N/A |
INTRINSIC |
|
low complexity region
|
378 |
394 |
N/A |
INTRINSIC |
|
low complexity region
|
456 |
468 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.0846 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.5%
|
| Validation Efficiency |
100% (45/45) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X2, X3, and X5. It has been shown to interact with itself as well as with regulatory factors X2 and X3, but it does not interact with regulatory factor X1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]
PHENOTYPE: Inactivating null allele or homozygous point mutation alleles exhibit missing dorsal midline structure of the cortex including the subcommissural organ and neonatal lethality. Heterozygous null mice have congenital hydrocephalus. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 47 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Angpt4 |
C |
T |
2: 151,780,892 (GRCm39) |
T380M |
probably damaging |
Het |
| Ankrd50 |
A |
T |
3: 38,537,172 (GRCm39) |
N60K |
probably damaging |
Het |
| Atp6v0a4 |
G |
A |
6: 38,059,048 (GRCm39) |
T245I |
probably benign |
Het |
| Calcoco2 |
TCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC |
TCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC |
11: 95,990,862 (GRCm39) |
|
probably null |
Het |
| Cyp2j13 |
T |
C |
4: 95,950,170 (GRCm39) |
D277G |
probably damaging |
Het |
| Def8 |
A |
T |
8: 124,185,105 (GRCm39) |
I310F |
probably benign |
Het |
| Dmtf1 |
A |
G |
5: 9,171,927 (GRCm39) |
L503S |
possibly damaging |
Het |
| Dock1 |
T |
C |
7: 134,770,125 (GRCm39) |
V1795A |
probably benign |
Het |
| Dusp9 |
TAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAG |
TAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAG |
X: 72,684,217 (GRCm39) |
|
probably benign |
Het |
| Gabbr1 |
A |
G |
17: 37,381,605 (GRCm39) |
T790A |
probably damaging |
Het |
| Glg1 |
C |
T |
8: 111,914,425 (GRCm39) |
R453Q |
probably benign |
Het |
| Gm10549 |
C |
T |
18: 33,597,375 (GRCm39) |
P54S |
unknown |
Het |
| Gpld1 |
G |
A |
13: 25,163,712 (GRCm39) |
V502I |
probably benign |
Het |
| Ifnar1 |
C |
T |
16: 91,292,367 (GRCm39) |
P207L |
probably benign |
Het |
| Inhba |
A |
G |
13: 16,191,966 (GRCm39) |
H29R |
probably benign |
Het |
| Insr |
G |
C |
8: 3,208,717 (GRCm39) |
P1248R |
probably damaging |
Het |
| Ipcef1 |
C |
T |
10: 6,840,663 (GRCm39) |
D349N |
probably damaging |
Het |
| Itga4 |
T |
A |
2: 79,156,004 (GRCm39) |
I990N |
possibly damaging |
Het |
| Malrd1 |
T |
C |
2: 15,618,988 (GRCm39) |
V284A |
|
Het |
| Maml2 |
C |
T |
9: 13,532,969 (GRCm39) |
Q728* |
probably null |
Het |
| Mex3d |
A |
T |
10: 80,217,581 (GRCm39) |
N545K |
|
Het |
| Mios |
T |
A |
6: 8,214,894 (GRCm39) |
V30E |
probably benign |
Het |
| Muc16 |
A |
G |
9: 18,449,060 (GRCm39) |
|
probably null |
Het |
| Naxd |
A |
G |
8: 11,562,968 (GRCm39) |
K303E |
possibly damaging |
Het |
| Or2w1 |
T |
C |
13: 21,317,865 (GRCm39) |
F307L |
probably benign |
Het |
| Or4l1 |
T |
C |
14: 50,166,906 (GRCm39) |
T32A |
probably benign |
Het |
| Or5a21 |
T |
A |
19: 12,310,803 (GRCm39) |
H139L |
possibly damaging |
Het |
| Or9q2 |
C |
T |
19: 13,772,200 (GRCm39) |
M258I |
probably damaging |
Het |
| Ovgp1 |
T |
C |
3: 105,893,883 (GRCm39) |
|
probably benign |
Het |
| Pknox1 |
C |
T |
17: 31,822,229 (GRCm39) |
T332M |
possibly damaging |
Het |
| Ptgdr |
A |
G |
14: 45,090,715 (GRCm39) |
S348P |
|
Het |
| Ptpdc1 |
T |
A |
13: 48,740,030 (GRCm39) |
E467V |
probably benign |
Het |
| Qsox1 |
A |
G |
1: 155,658,343 (GRCm39) |
S409P |
probably damaging |
Het |
| Slc30a5 |
T |
C |
13: 100,949,970 (GRCm39) |
T371A |
probably damaging |
Het |
| Slc5a7 |
A |
T |
17: 54,583,669 (GRCm39) |
N540K |
probably benign |
Het |
| Slco6c1 |
A |
T |
1: 96,990,248 (GRCm39) |
S664R |
possibly damaging |
Het |
| Tbxa2r |
A |
G |
10: 81,168,958 (GRCm39) |
S216G |
probably damaging |
Het |
| Tgm4 |
C |
A |
9: 122,881,837 (GRCm39) |
S344R |
probably damaging |
Het |
| Thoc6 |
A |
G |
17: 23,887,823 (GRCm39) |
V328A |
possibly damaging |
Het |
| Trim61 |
T |
A |
8: 65,467,228 (GRCm39) |
Q11L |
probably damaging |
Het |
| Txndc2 |
G |
A |
17: 65,944,992 (GRCm39) |
T395I |
probably damaging |
Het |
| Txndc9 |
T |
C |
1: 38,034,859 (GRCm39) |
E15G |
probably benign |
Het |
| Unc93a2 |
G |
T |
17: 7,641,842 (GRCm39) |
T202K |
probably damaging |
Het |
| Uspl1 |
G |
A |
5: 149,146,481 (GRCm39) |
V411M |
probably damaging |
Het |
| Vcpip1 |
A |
G |
1: 9,816,049 (GRCm39) |
I778T |
possibly damaging |
Het |
| Vps54 |
A |
G |
11: 21,242,108 (GRCm39) |
T408A |
probably benign |
Het |
| Wscd1 |
T |
C |
11: 71,650,799 (GRCm39) |
L42P |
possibly damaging |
Het |
|
| Other mutations in Rfx4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00094:Rfx4
|
APN |
10 |
84,676,063 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00334:Rfx4
|
APN |
10 |
84,615,917 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
IGL00928:Rfx4
|
APN |
10 |
84,675,978 (GRCm39) |
missense |
probably benign |
0.04 |
|
IGL01063:Rfx4
|
APN |
10 |
84,704,246 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
IGL01490:Rfx4
|
APN |
10 |
84,676,715 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
IGL02390:Rfx4
|
APN |
10 |
84,676,014 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02454:Rfx4
|
APN |
10 |
84,675,970 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R0099:Rfx4
|
UTSW |
10 |
84,730,168 (GRCm39) |
missense |
probably benign |
|
|
R0503:Rfx4
|
UTSW |
10 |
84,730,196 (GRCm39) |
missense |
possibly damaging |
0.56 |
|
R0924:Rfx4
|
UTSW |
10 |
84,704,291 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0930:Rfx4
|
UTSW |
10 |
84,704,291 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1386:Rfx4
|
UTSW |
10 |
84,699,149 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1715:Rfx4
|
UTSW |
10 |
84,680,144 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1738:Rfx4
|
UTSW |
10 |
84,716,839 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1987:Rfx4
|
UTSW |
10 |
84,731,952 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R3717:Rfx4
|
UTSW |
10 |
84,716,088 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4231:Rfx4
|
UTSW |
10 |
84,650,558 (GRCm39) |
missense |
probably benign |
0.03 |
|
R4300:Rfx4
|
UTSW |
10 |
84,740,966 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4581:Rfx4
|
UTSW |
10 |
84,680,164 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R4582:Rfx4
|
UTSW |
10 |
84,680,164 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R4618:Rfx4
|
UTSW |
10 |
84,716,760 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5156:Rfx4
|
UTSW |
10 |
84,704,218 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5185:Rfx4
|
UTSW |
10 |
84,699,114 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5377:Rfx4
|
UTSW |
10 |
84,696,406 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R5601:Rfx4
|
UTSW |
10 |
84,634,442 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5879:Rfx4
|
UTSW |
10 |
84,650,625 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5996:Rfx4
|
UTSW |
10 |
84,675,881 (GRCm39) |
nonsense |
probably null |
|
|
R6358:Rfx4
|
UTSW |
10 |
84,680,099 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6805:Rfx4
|
UTSW |
10 |
84,676,092 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R7248:Rfx4
|
UTSW |
10 |
84,740,919 (GRCm39) |
missense |
probably benign |
0.05 |
|
R7427:Rfx4
|
UTSW |
10 |
84,731,876 (GRCm39) |
missense |
probably benign |
0.28 |
|
R7428:Rfx4
|
UTSW |
10 |
84,731,876 (GRCm39) |
missense |
probably benign |
0.28 |
|
R7514:Rfx4
|
UTSW |
10 |
84,716,090 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7576:Rfx4
|
UTSW |
10 |
84,699,213 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8002:Rfx4
|
UTSW |
10 |
84,676,721 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R8838:Rfx4
|
UTSW |
10 |
84,676,758 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8938:Rfx4
|
UTSW |
10 |
84,675,936 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9513:Rfx4
|
UTSW |
10 |
84,674,050 (GRCm39) |
start codon destroyed |
probably null |
0.01 |
|
RF010:Rfx4
|
UTSW |
10 |
84,694,351 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
RF014:Rfx4
|
UTSW |
10 |
84,694,353 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
RF015:Rfx4
|
UTSW |
10 |
84,694,353 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
RF023:Rfx4
|
UTSW |
10 |
84,694,349 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
RF030:Rfx4
|
UTSW |
10 |
84,694,344 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
RF035:Rfx4
|
UTSW |
10 |
84,694,344 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
RF046:Rfx4
|
UTSW |
10 |
84,694,345 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
RF060:Rfx4
|
UTSW |
10 |
84,694,358 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
RF062:Rfx4
|
UTSW |
10 |
84,694,345 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
X0024:Rfx4
|
UTSW |
10 |
84,615,938 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
Z1177:Rfx4
|
UTSW |
10 |
84,731,955 (GRCm39) |
missense |
probably benign |
0.30 |
|
Z1177:Rfx4
|
UTSW |
10 |
84,650,548 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGTTCCATCAACTCCCGAGAATAG -3'
(R):5'- ATGAAAGCAGTCACTTAGCCC -3'
Sequencing Primer
(F):5'- CTCCCGAGAATAGCGTCTTGAAATG -3'
(R):5'- AGTCACTTAGCCCATCCAGTG -3'
|
| Posted On |
2022-04-18 |
Incidental Mutation