Incidental Mutation 'R0468:Safb'
| ID |
41771 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Safb
|
| Ensembl Gene |
ENSMUSG00000071054 |
| Gene Name |
scaffold attachment factor B |
| Synonyms |
5330423C17Rik, SAFB1, 3110021E02Rik |
| MMRRC Submission |
038668-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.757)
|
| Stock # |
R0468 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
56891982-56913294 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 56913025 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Cysteine
at position 914
(R914C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000138277
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000052832]
[ENSMUST00000095224]
[ENSMUST00000182533]
|
| AlphaFold |
D3YXK2 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000052832
|
| SMART Domains |
Protein: ENSMUSP00000052908
Gene: ENSMUSG00000049760
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:QIL1
|
9 |
108 |
5.9e-29 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000095224
AA Change: R912C
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000092849
Gene: ENSMUSG00000071054
AA Change: R912C
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
11 |
24 |
N/A |
INTRINSIC |
|
SAP
|
31 |
65 |
7.15e-11 |
SMART |
|
coiled coil region
|
268 |
291 |
N/A |
INTRINSIC |
|
low complexity region
|
292 |
300 |
N/A |
INTRINSIC |
|
RRM
|
429 |
502 |
3.76e-19 |
SMART |
|
coiled coil region
|
651 |
728 |
N/A |
INTRINSIC |
|
low complexity region
|
760 |
778 |
N/A |
INTRINSIC |
|
low complexity region
|
885 |
898 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000182378
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000182454
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000182461
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000182533
AA Change: R914C
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000138277
Gene: ENSMUSG00000071054
AA Change: R914C
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
11 |
24 |
N/A |
INTRINSIC |
|
SAP
|
31 |
65 |
7.15e-11 |
SMART |
|
coiled coil region
|
268 |
291 |
N/A |
INTRINSIC |
|
low complexity region
|
292 |
300 |
N/A |
INTRINSIC |
|
RRM
|
429 |
502 |
3.76e-19 |
SMART |
|
coiled coil region
|
651 |
728 |
N/A |
INTRINSIC |
|
low complexity region
|
760 |
778 |
N/A |
INTRINSIC |
|
low complexity region
|
831 |
842 |
N/A |
INTRINSIC |
|
low complexity region
|
887 |
900 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000182913
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000183041
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000183318
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000182951
|
| Meta Mutation Damage Score |
0.6467 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.2%
|
| Validation Efficiency |
100% (61/61) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a DNA-binding protein which has high specificity for scaffold or matrix attachment region DNA elements (S/MAR DNA). This protein is thought to be involved in attaching the base of chromatin loops to the nuclear matrix but there is conflicting evidence as to whether this protein is a component of chromatin or a nuclear matrix protein. Scaffold attachment factors are a specific subset of nuclear matrix proteins (NMP) that specifically bind to S/MAR. The encoded protein is thought to serve as a molecular base to assemble a 'transcriptosome complex' in the vicinity of actively transcribed genes. It is involved in the regulation of heat shock protein 27 transcription, can act as an estrogen receptor co-repressor and is a candidate for breast tumorigenesis. This gene is arranged head-to-head with a similar gene whose product has the same functions. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]
PHENOTYPE: Homozygous null mice display partial embryonic and neonatal lethality, neonatal cyanosis, impaired embryonic hematopoiesis, male sterility, azoospermia, reduced female fertility, impaired transport of embryos through the oviduct, reduced embryonic growth, testicular degeneration and ovarian atrophy. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 56 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2700049A03Rik |
A |
G |
12: 71,240,084 (GRCm39) |
H1298R |
possibly damaging |
Het |
| 5530400C23Rik |
T |
C |
6: 133,271,421 (GRCm39) |
L155P |
probably benign |
Het |
| 6820408C15Rik |
A |
T |
2: 152,283,186 (GRCm39) |
R283S |
probably benign |
Het |
| Aldh1l2 |
T |
A |
10: 83,354,542 (GRCm39) |
E104D |
probably benign |
Het |
| Anxa3 |
T |
C |
5: 96,958,958 (GRCm39) |
V22A |
probably benign |
Het |
| Bcl7b |
T |
C |
5: 135,209,737 (GRCm39) |
F188L |
probably benign |
Het |
| Brinp1 |
T |
A |
4: 68,681,013 (GRCm39) |
I506F |
probably damaging |
Het |
| Bsdc1 |
T |
C |
4: 129,355,511 (GRCm39) |
|
probably benign |
Het |
| Ccdc180 |
T |
C |
4: 45,923,271 (GRCm39) |
I1075T |
possibly damaging |
Het |
| Cep162 |
A |
G |
9: 87,075,750 (GRCm39) |
L1294P |
probably damaging |
Het |
| Cltc |
G |
A |
11: 86,595,452 (GRCm39) |
|
probably benign |
Het |
| Col11a1 |
T |
C |
3: 114,010,707 (GRCm39) |
|
probably benign |
Het |
| Col14a1 |
A |
T |
15: 55,252,042 (GRCm39) |
Y566F |
unknown |
Het |
| Dhx29 |
A |
G |
13: 113,099,811 (GRCm39) |
Q1148R |
probably benign |
Het |
| Ehbp1 |
A |
G |
11: 22,119,184 (GRCm39) |
|
probably benign |
Het |
| Ehd3 |
A |
G |
17: 74,112,374 (GRCm39) |
H46R |
probably damaging |
Het |
| Fam171a1 |
T |
C |
2: 3,226,433 (GRCm39) |
V522A |
probably benign |
Het |
| Gm4553 |
C |
A |
7: 141,719,362 (GRCm39) |
C22F |
unknown |
Het |
| Hibadh |
C |
T |
6: 52,534,755 (GRCm39) |
|
probably benign |
Het |
| Hspg2 |
G |
A |
4: 137,260,840 (GRCm39) |
C1613Y |
probably damaging |
Het |
| Hydin |
G |
T |
8: 111,139,855 (GRCm39) |
C708F |
possibly damaging |
Het |
| Ifi208 |
A |
T |
1: 173,511,047 (GRCm39) |
M401L |
probably benign |
Het |
| Igsf8 |
G |
A |
1: 172,146,363 (GRCm39) |
V454M |
probably damaging |
Het |
| Irx4 |
G |
T |
13: 73,414,839 (GRCm39) |
|
probably benign |
Het |
| Kcnh4 |
C |
T |
11: 100,637,758 (GRCm39) |
G633E |
probably benign |
Het |
| Kcnn2 |
C |
T |
18: 45,692,538 (GRCm39) |
T38M |
possibly damaging |
Het |
| L3mbtl3 |
C |
T |
10: 26,203,630 (GRCm39) |
R400H |
unknown |
Het |
| Lrp6 |
T |
C |
6: 134,462,624 (GRCm39) |
T679A |
possibly damaging |
Het |
| Map9 |
T |
C |
3: 82,281,510 (GRCm39) |
|
probably null |
Het |
| Men1 |
T |
A |
19: 6,386,953 (GRCm39) |
V5E |
probably null |
Het |
| Mettl14 |
T |
C |
3: 123,165,061 (GRCm39) |
D93G |
probably damaging |
Het |
| Neb |
G |
T |
2: 52,101,568 (GRCm39) |
R4601S |
probably damaging |
Het |
| Nell1 |
A |
G |
7: 49,878,594 (GRCm39) |
T272A |
probably damaging |
Het |
| Or10ag53 |
A |
T |
2: 87,082,599 (GRCm39) |
N106I |
probably benign |
Het |
| Or2ak6 |
A |
T |
11: 58,592,619 (GRCm39) |
I31F |
probably damaging |
Het |
| Pclo |
C |
A |
5: 14,727,302 (GRCm39) |
|
probably benign |
Het |
| Pdia5 |
A |
G |
16: 35,217,877 (GRCm39) |
L502P |
probably damaging |
Het |
| Pkd1l3 |
C |
G |
8: 110,350,281 (GRCm39) |
D375E |
possibly damaging |
Het |
| Plxna4 |
C |
A |
6: 32,192,181 (GRCm39) |
C803F |
probably damaging |
Het |
| Pmfbp1 |
A |
G |
8: 110,240,600 (GRCm39) |
|
probably null |
Het |
| Ptgs1 |
A |
G |
2: 36,139,205 (GRCm39) |
Y468C |
probably damaging |
Het |
| Pxdn |
G |
T |
12: 30,044,485 (GRCm39) |
G488W |
probably damaging |
Het |
| Sec31b |
T |
A |
19: 44,506,947 (GRCm39) |
|
probably benign |
Het |
| Shank3 |
G |
A |
15: 89,433,478 (GRCm39) |
V1333I |
probably benign |
Het |
| Slamf1 |
A |
G |
1: 171,619,939 (GRCm39) |
|
probably benign |
Het |
| Slc23a3 |
T |
A |
1: 75,109,874 (GRCm39) |
Q131L |
possibly damaging |
Het |
| Slc7a11 |
A |
G |
3: 50,338,500 (GRCm39) |
V303A |
probably damaging |
Het |
| Slc7a13 |
T |
A |
4: 19,841,500 (GRCm39) |
V449D |
probably benign |
Het |
| Srp68 |
A |
T |
11: 116,139,590 (GRCm39) |
I453K |
probably damaging |
Het |
| Steap3 |
A |
T |
1: 120,162,030 (GRCm39) |
V414D |
probably damaging |
Het |
| Tagln2 |
A |
G |
1: 172,333,788 (GRCm39) |
N131D |
probably benign |
Het |
| Tmem132d |
T |
C |
5: 128,346,267 (GRCm39) |
Y85C |
probably damaging |
Het |
| Vcam1 |
A |
T |
3: 115,909,595 (GRCm39) |
Y577* |
probably null |
Het |
| Vmn1r214 |
A |
G |
13: 23,219,423 (GRCm39) |
T306A |
probably benign |
Het |
| Zfyve1 |
A |
T |
12: 83,602,048 (GRCm39) |
|
probably benign |
Het |
| Zgrf1 |
T |
A |
3: 127,355,690 (GRCm39) |
N305K |
possibly damaging |
Het |
|
| Other mutations in Safb |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01465:Safb
|
APN |
17 |
56,909,974 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02391:Safb
|
APN |
17 |
56,907,813 (GRCm39) |
splice site |
probably benign |
|
|
IGL03145:Safb
|
APN |
17 |
56,912,287 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0245:Safb
|
UTSW |
17 |
56,913,025 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0464:Safb
|
UTSW |
17 |
56,913,025 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0479:Safb
|
UTSW |
17 |
56,913,025 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0496:Safb
|
UTSW |
17 |
56,912,630 (GRCm39) |
missense |
probably benign |
0.05 |
|
R0639:Safb
|
UTSW |
17 |
56,908,092 (GRCm39) |
utr 3 prime |
probably benign |
|
|
R0655:Safb
|
UTSW |
17 |
56,904,803 (GRCm39) |
missense |
probably benign |
0.23 |
|
R1109:Safb
|
UTSW |
17 |
56,908,228 (GRCm39) |
splice site |
probably benign |
|
|
R1941:Safb
|
UTSW |
17 |
56,905,992 (GRCm39) |
intron |
probably benign |
|
|
R1969:Safb
|
UTSW |
17 |
56,912,821 (GRCm39) |
missense |
probably benign |
0.32 |
|
R1971:Safb
|
UTSW |
17 |
56,912,821 (GRCm39) |
missense |
probably benign |
0.32 |
|
R4010:Safb
|
UTSW |
17 |
56,910,765 (GRCm39) |
unclassified |
probably benign |
|
|
R4132:Safb
|
UTSW |
17 |
56,907,848 (GRCm39) |
utr 3 prime |
probably benign |
|
|
R5429:Safb
|
UTSW |
17 |
56,895,822 (GRCm39) |
missense |
probably benign |
0.15 |
|
R5681:Safb
|
UTSW |
17 |
56,906,000 (GRCm39) |
intron |
probably benign |
|
|
R5900:Safb
|
UTSW |
17 |
56,907,349 (GRCm39) |
missense |
unknown |
|
|
R6077:Safb
|
UTSW |
17 |
56,909,956 (GRCm39) |
unclassified |
probably benign |
|
|
R6173:Safb
|
UTSW |
17 |
56,904,798 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6367:Safb
|
UTSW |
17 |
56,900,845 (GRCm39) |
unclassified |
probably benign |
|
|
R6735:Safb
|
UTSW |
17 |
56,892,169 (GRCm39) |
unclassified |
probably benign |
|
|
R6736:Safb
|
UTSW |
17 |
56,913,023 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R7699:Safb
|
UTSW |
17 |
56,908,504 (GRCm39) |
missense |
unknown |
|
|
R7834:Safb
|
UTSW |
17 |
56,900,881 (GRCm39) |
missense |
unknown |
|
|
R7909:Safb
|
UTSW |
17 |
56,902,665 (GRCm39) |
missense |
unknown |
|
|
R8167:Safb
|
UTSW |
17 |
56,892,286 (GRCm39) |
missense |
unknown |
|
|
R8810:Safb
|
UTSW |
17 |
56,910,579 (GRCm39) |
missense |
unknown |
|
|
X0065:Safb
|
UTSW |
17 |
56,910,798 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTGCCAAACTGCCCACTTGGAC -3'
(R):5'- GGCTGATGGTAGAGTGCCACTTTC -3'
Sequencing Primer
(F):5'- GGCCTGGTCACATGATGAAC -3'
(R):5'- TAGGACTTGAAGGTCACGGT -3'
|
| Posted On |
2013-05-23 |
Incidental Mutation