Incidental Mutation 'RF060:Rfx4'
| ID |
605387 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rfx4
|
| Ensembl Gene |
ENSMUSG00000020037 |
| Gene Name |
regulatory factor X, 4 (influences HLA class II expression) |
| Synonyms |
4933412G19Rik |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
RF060 (G1)
|
| Quality Score |
217.468 |
|
Status
|
Not validated
|
| Chromosome |
10 |
| Chromosomal Location |
84591926-84742402 bp(+) (GRCm39) |
| Type of Mutation |
critical splice acceptor site |
| DNA Base Change (assembly) |
T to TCTCTCTCTCTCTCTCC
at 84694358 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000051107
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000060397]
[ENSMUST00000095388]
[ENSMUST00000166696]
|
| AlphaFold |
Q7TNK1 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000060397
|
| SMART Domains |
Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
| 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
|
| SMART Domains |
Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
| 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
|
| SMART Domains |
Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
| 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 |
|
| Coding Region Coverage |
- 1x: 99.8%
- 3x: 99.7%
- 10x: 99.3%
- 20x: 98.7%
|
| Validation Efficiency |
|
| 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: 34 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A030005L19Rik |
TTGCTGTGGCTGTGGAGGTTGTGGCGGCTGTGGCTGTGG |
TGGCTGTGGCTGTGG |
1: 82,891,117 (GRCm39) |
|
probably benign |
Het |
| A030005L19Rik |
GCTG |
GCTGTGGCTTCTG |
1: 82,891,308 (GRCm39) |
|
probably benign |
Het |
| A030005L19Rik |
CTGTGGCTG |
CTGTGGCTGATGTGGCTG |
1: 82,891,300 (GRCm39) |
|
probably null |
Het |
| Ankhd1 |
G |
GTGGCGC |
18: 36,693,975 (GRCm39) |
|
probably benign |
Het |
| Cacna1f |
GAG |
GAGCAG |
X: 7,486,299 (GRCm39) |
|
probably benign |
Het |
| Cd109 |
ATTTATTTAT |
ATTTATTTATTTCTTTATTTAT |
9: 78,619,807 (GRCm39) |
|
probably benign |
Het |
| Chd4 |
CC |
CCACTGGC |
6: 125,099,108 (GRCm39) |
|
probably benign |
Het |
| Chga |
GCA |
GCATCA |
12: 102,527,683 (GRCm39) |
|
probably benign |
Het |
| Cyb5r4 |
ACTGCCCAGGGATGTGACAGACACACTGCCCAGGGA |
ACTGCCCAGGGATCTGACAGACACGCTGCCCAGGGATGTGACAGACACACTGCCCAGGGA |
9: 86,922,466 (GRCm39) |
|
probably benign |
Het |
| Dnmt1 |
CGTT |
CGTTGTGGGGGAGGAGCACAGTTCCTACCTAGTT |
9: 20,821,438 (GRCm39) |
|
probably null |
Het |
| Fam171b |
GC |
GCCGCAAC |
2: 83,643,221 (GRCm39) |
|
probably benign |
Het |
| Fkbp1a |
GCCGCCGCCA |
G |
2: 151,384,619 (GRCm39) |
|
probably null |
Het |
| Gab3 |
TTC |
TTCCTC |
X: 74,043,619 (GRCm39) |
|
probably benign |
Het |
| Garin5a |
GTCTGAGGGAGGA |
GTCTGAGGGAGGAAGGCTGGATCCTGGATACCTGGTTCTGAGGGAGGA |
7: 44,149,949 (GRCm39) |
|
probably null |
Het |
| Garin5a |
GAGGA |
GAGGAAGGCTGGATCCTGGATACCTGGGTCTGAGGTAGGA |
7: 44,149,957 (GRCm39) |
|
probably null |
Het |
| Hsdl2 |
AAGCCACAGCTGCAGGAGAAGCCACAGCTGCAGGAGCAGCCACAGCTGCAGGAGAAGCCACAGCTGCAGGAGCAGCCACAGC |
AAGCCACAGCTGCAGGAGCAGCCACAGCTGCAGGAGAAGCCACAGCTGCAGGAGCAGCCACAGCTGCAGGAGAAGCCACAGCTGCAGGAGCAGCCACAGC |
4: 59,610,608 (GRCm39) |
|
probably benign |
Het |
| Klra10 |
TGTAGT |
TGT |
6: 130,252,784 (GRCm39) |
|
probably benign |
Het |
| L1td1 |
GAGGAGGAGGAGGAGGAGGGGGAGGAGGAGAAGGAGGA |
GAGGAGGA |
4: 98,625,031 (GRCm39) |
|
probably benign |
Het |
| Mamld1 |
CAG |
CAGTAG |
X: 70,162,437 (GRCm39) |
|
probably null |
Het |
| Mamld1 |
AGC |
AGCCGC |
X: 70,162,438 (GRCm39) |
|
probably benign |
Het |
| Map1a |
A |
AGCTCCAGCTCCAGCTCCAGCTCCAGCTCCC |
2: 121,136,799 (GRCm39) |
|
probably benign |
Het |
| Nefh |
GACTTGGCC |
GACTTGGCCCCACCTGGGTACTTGGCC |
11: 4,891,050 (GRCm39) |
|
probably benign |
Het |
| Nefh |
CT |
CTGGGCTTCACCTGGGGATT |
11: 4,891,052 (GRCm39) |
|
probably benign |
Het |
| Pdk1 |
CTGGCCT |
C |
2: 71,703,789 (GRCm39) |
|
probably benign |
Het |
| Pou3f1 |
GC |
GCGGCGCC |
4: 124,551,602 (GRCm39) |
|
probably benign |
Het |
| Spaca1 |
CTCGCT |
CTCGCTGTCGCT |
4: 34,049,841 (GRCm39) |
|
probably benign |
Het |
| Spmap2l |
CAG |
CAGCGATCCTCCCCAGTCCCGCAAGGCAAG |
5: 77,164,274 (GRCm39) |
|
probably benign |
Het |
| St3gal5 |
G |
GCACTC |
6: 72,074,836 (GRCm39) |
|
probably null |
Het |
| Stat1 |
G |
T |
1: 52,191,419 (GRCm39) |
E591D |
probably benign |
Het |
| Tcof1 |
CAG |
CAGTAG |
18: 60,968,816 (GRCm39) |
|
probably benign |
Het |
| Tcof1 |
C |
CAGT |
18: 60,968,819 (GRCm39) |
|
probably benign |
Het |
| Tfeb |
GCA |
GCACCA |
17: 48,097,031 (GRCm39) |
|
probably benign |
Het |
| Tmem59 |
TTTGTTT |
TTTGTTTGCTTGTTT |
4: 107,047,723 (GRCm39) |
|
probably benign |
Het |
| Zfhx3 |
G |
GAAACAGCAA |
8: 109,682,720 (GRCm39) |
|
probably benign |
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 |
|
R9359:Rfx4
|
UTSW |
10 |
84,740,921 (GRCm39) |
missense |
probably benign |
0.00 |
|
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 |
|
|
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'- CCGAAGTGACCAGATCTTCAAAG -3'
(R):5'- GCACATGGGAAACACTTAGCC -3'
Sequencing Primer
(F):5'- GTGACCAGATCTTCAAAGGCACAG -3'
(R):5'- TGGGAAACACTTAGCCTAATTCTGGG -3'
|
| Posted On |
2019-12-04 |
Incidental Mutation