Mutagenetix > Incidental Mutation

Incidental Mutation 'R0464:Safb'

71456

Institutional Source

Beutler Lab

Gene Symbol

Safb

Ensembl Gene

ENSMUSG00000071054

Gene Name

scaffold attachment factor B

Synonyms

5330423C17Rik, SAFB1, 3110021E02Rik

MMRRC Submission

038664-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.757) question?

Stock #

R0464 (G1)

Quality Score

225

Status

Validated

Chromosome

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: 99.3%
3x: 98.7%
10x: 97.3%
20x: 94.7%

Validation Efficiency

100% (80/80)

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: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ada	G	T	2: 163,574,884 (GRCm39)	Y84*	probably null	Het
Adar	T	A	3: 89,642,889 (GRCm39)	C257S	possibly damaging	Het
Adgrd1	G	T	5: 129,239,714 (GRCm39)	C507F	probably damaging	Het
Atp5f1a	T	C	18: 77,867,622 (GRCm39)	Y299H	probably benign	Het
Bok	G	T	1: 93,621,935 (GRCm39)	R77L	probably damaging	Het
Cdx2	C	A	5: 147,243,283 (GRCm39)	K170N	possibly damaging	Het
Ceacam1	A	G	7: 25,171,442 (GRCm39)	S341P	possibly damaging	Het
Cfhr3	A	T	1: 139,521,683 (GRCm39)		noncoding transcript	Het
Ckap5	A	G	2: 91,409,858 (GRCm39)	I947V	probably benign	Het
Clec2i	T	C	6: 128,872,386 (GRCm39)	Y173H	probably damaging	Het
Cttnbp2	T	C	6: 18,408,690 (GRCm39)	D977G	possibly damaging	Het
Cyp2f2	C	A	7: 26,831,962 (GRCm39)	Q406K	probably benign	Het
Ddx28	A	G	8: 106,736,685 (GRCm39)	S458P	probably damaging	Het
Dppa3	T	A	6: 122,605,492 (GRCm39)		probably null	Het
Dusp10	C	A	1: 183,801,273 (GRCm39)	L347I	probably benign	Het
Fads1	C	T	19: 10,160,429 (GRCm39)	P5L	probably benign	Het
Fbxl15	A	T	19: 46,316,951 (GRCm39)	E13D	probably benign	Het
Fhit	T	A	14: 10,991,567 (GRCm38)		probably benign	Het
Fras1	G	T	5: 96,784,662 (GRCm39)	V882F	probably damaging	Het
G3bp1	T	C	11: 55,389,452 (GRCm39)	F383L	probably damaging	Het
Gabbr1	C	T	17: 37,361,726 (GRCm39)		probably benign	Het
Ganc	T	A	2: 120,267,175 (GRCm39)	V497D	probably benign	Het
Glt8d2	T	G	10: 82,490,564 (GRCm39)	H242P	possibly damaging	Het
Gna15	T	C	10: 81,348,338 (GRCm39)	Y131C	probably benign	Het
Gpatch8	T	C	11: 102,371,712 (GRCm39)	K609E	unknown	Het
Gprc5a	A	T	6: 135,056,413 (GRCm39)	K287*	probably null	Het
Iqub	T	A	6: 24,479,262 (GRCm39)	K427*	probably null	Het
Itpr2	C	G	6: 146,277,387 (GRCm39)	D666H	probably damaging	Het
Kcnj5	T	C	9: 32,234,269 (GRCm39)	I15M	possibly damaging	Het
Kcnn2	A	G	18: 45,693,426 (GRCm39)	E334G	probably damaging	Het
Lypd6	T	A	2: 50,080,690 (GRCm39)	I126N	probably damaging	Het
Ms4a20	A	G	19: 11,089,801 (GRCm39)	L28P	probably damaging	Het
Mtus1	T	C	8: 41,455,511 (GRCm39)	D56G	probably damaging	Het
Myo1h	A	G	5: 114,498,571 (GRCm39)	D889G	probably damaging	Het
Myrf	G	C	19: 10,195,526 (GRCm39)	T428S	probably benign	Het
Nab1	T	C	1: 52,529,174 (GRCm39)	D241G	possibly damaging	Het
Naip2	A	C	13: 100,298,290 (GRCm39)	I582S	probably benign	Het
Ncbp3	C	T	11: 72,960,647 (GRCm39)		probably benign	Het
Nek1	T	A	8: 61,525,307 (GRCm39)		probably benign	Het
Nf1	T	C	11: 79,447,615 (GRCm39)	V2452A	probably benign	Het
Nlrp1b	A	C	11: 71,109,070 (GRCm39)	S144A	probably damaging	Het
Npr2	A	T	4: 43,640,597 (GRCm39)		probably null	Het
Pak3	TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC	"TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC"	X: 142,526,889 (GRCm39)		probably benign	Het
Paox	T	A	7: 139,709,195 (GRCm39)		probably benign	Het
Pcdh15	T	A	10: 74,462,676 (GRCm39)		probably null	Het
Pde8b	G	A	13: 95,241,206 (GRCm39)	T202M	probably damaging	Het
Pigo	A	T	4: 43,019,814 (GRCm39)	V905D	probably benign	Het
Pik3cb	A	G	9: 98,926,796 (GRCm39)		probably null	Het
Rassf5	T	C	1: 131,139,998 (GRCm39)	N87S	probably benign	Het
Rbl1	C	A	2: 156,989,465 (GRCm39)	K1051N	probably damaging	Het
Rfx7	T	C	9: 72,525,486 (GRCm39)	V892A	probably damaging	Het
Ripply1	TTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT	TTCCTCCTCCTCCTCCTCCTCCTCCTCCT	X: 138,680,599 (GRCm39)		probably benign	Het
Rnf144b	T	A	13: 47,396,363 (GRCm39)	Y233*	probably null	Het
Sbf2	T	C	7: 110,063,783 (GRCm39)		probably benign	Het
Sgo2a	A	T	1: 58,039,253 (GRCm39)	K85N	probably damaging	Het
Siglec1	A	T	2: 130,921,279 (GRCm39)	C631S	probably damaging	Het
Simc1	C	T	13: 54,684,913 (GRCm39)	R50*	probably null	Het
Skint5	T	A	4: 113,392,928 (GRCm39)	M1235L	unknown	Het
Slc22a19	A	T	19: 7,660,278 (GRCm39)	N377K	probably benign	Het
Spata31d1a	A	G	13: 59,849,573 (GRCm39)	F852L	possibly damaging	Het
Spata31e3	A	G	13: 50,402,311 (GRCm39)		probably benign	Het
Srbd1	G	A	17: 86,427,430 (GRCm39)	S401F	probably damaging	Het
Stk36	C	A	1: 74,650,331 (GRCm39)	Q288K	probably damaging	Het
Styx	T	C	14: 45,609,908 (GRCm39)	S191P	probably benign	Het
Supt6	T	A	11: 78,107,164 (GRCm39)	N1214I	probably benign	Het
Tcim	T	A	8: 24,928,644 (GRCm39)	D90V	probably damaging	Het
Tdpoz1	T	A	3: 93,578,782 (GRCm39)	M1L	probably damaging	Het
Tep1	T	A	14: 51,085,141 (GRCm39)	T881S	probably benign	Het
Tlr5	C	T	1: 182,801,275 (GRCm39)	A193V	probably benign	Het
Tmem117	T	A	15: 94,612,800 (GRCm39)	F112Y	probably damaging	Het
Tnrc6c	C	T	11: 117,651,375 (GRCm39)	R1633W	probably damaging	Het
Trh	T	C	6: 92,220,649 (GRCm39)		probably null	Het
Triobp	A	G	15: 78,851,186 (GRCm39)	R447G	possibly damaging	Het
Trip6	A	G	5: 137,311,943 (GRCm39)	F46S	probably damaging	Het
Ubxn4	G	A	1: 128,190,641 (GRCm39)	E256K	probably benign	Het
Usp33	T	C	3: 152,081,872 (GRCm39)		probably benign	Het
Vmn2r60	A	T	7: 41,785,255 (GRCm39)	I156F	probably damaging	Het
Wdr17	T	C	8: 55,123,427 (GRCm39)		probably benign	Het
Wdr35	G	T	12: 9,077,472 (GRCm39)		probably benign	Het
Wwp1	C	T	4: 19,638,763 (GRCm39)		probably benign	Het
Zfp652	T	C	11: 95,654,475 (GRCm39)	C293R	probably 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
R0468: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

2013-09-30