Mutagenetix > Incidental Mutation

Incidental Mutation 'R5429:Safb'

427099

Institutional Source

Beutler Lab

Gene Symbol

Safb

Ensembl Gene

ENSMUSG00000071054

Gene Name

scaffold attachment factor B

Synonyms

3110021E02Rik, SAFB1, 5330423C17Rik

MMRRC Submission

042995-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.787) question?

Stock #

R5429 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

56584825-56606294 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 56588822 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 20 (V20A)

Ref Sequence

ENSEMBL: ENSMUSP00000138743 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000075510] [ENSMUST00000095224] [ENSMUST00000133604] [ENSMUST00000144255] [ENSMUST00000155983] [ENSMUST00000182533] [ENSMUST00000182800]

AlphaFold

D3YXK2

Predicted Effect

probably benign
Transcript: ENSMUST00000075510

SMART Domains

Protein: ENSMUSP00000074953
Gene: ENSMUSG00000042625

Domain	Start	End	E-Value	Type
SAP	25	59	8.21e-11	SMART
low complexity region	91	104	N/A	INTRINSIC
low complexity region	162	173	N/A	INTRINSIC
coiled coil region	262	285	N/A	INTRINSIC
low complexity region	286	294	N/A	INTRINSIC
low complexity region	318	335	N/A	INTRINSIC
RRM	452	525	1.33e-19	SMART
low complexity region	557	578	N/A	INTRINSIC
low complexity region	631	645	N/A	INTRINSIC
coiled coil region	658	772	N/A	INTRINSIC
low complexity region	798	815	N/A	INTRINSIC
low complexity region	920	944	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000095224
AA Change: V77A

SMART Domains

Protein: ENSMUSP00000092849
Gene: ENSMUSG00000071054
AA Change: V77A

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

probably benign
Transcript: ENSMUST00000133604

SMART Domains

Protein: ENSMUSP00000119324
Gene: ENSMUSG00000042625

Domain	Start	End	E-Value	Type
SAP	25	59	8.21e-11	SMART
low complexity region	91	104	N/A	INTRINSIC
low complexity region	162	173	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000144255

SMART Domains

Protein: ENSMUSP00000123673
Gene: ENSMUSG00000042625

Domain	Start	End	E-Value	Type
SAP	25	59	8.21e-11	SMART
low complexity region	91	104	N/A	INTRINSIC
low complexity region	162	173	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146070

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146958

Predicted Effect

probably benign
Transcript: ENSMUST00000155983

SMART Domains

Protein: ENSMUSP00000116363
Gene: ENSMUSG00000042625

Domain	Start	End	E-Value	Type
SAP	25	59	8.21e-11	SMART
low complexity region	91	104	N/A	INTRINSIC
low complexity region	162	173	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000182031

Predicted Effect

unknown
Transcript: ENSMUST00000182533
AA Change: V77A

SMART Domains

Protein: ENSMUSP00000138277
Gene: ENSMUSG00000071054
AA Change: V77A

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

probably benign
Transcript: ENSMUST00000182800
AA Change: V20A

PolyPhen 2 Score 0.152 (Sensitivity: 0.92; Specificity: 0.87)

Predicted Effect

probably benign
Transcript: ENSMUST00000182951

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.0%

Validation Efficiency

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: 47 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410141K09Rik	G	A	13: 66,431,828	P199S	probably benign	Het
Akap13	T	G	7: 75,602,904	S261A	possibly damaging	Het
Ankrd34a	G	A	3: 96,597,521	G14R	probably damaging	Het
Auts2	G	A	5: 131,472,335	T289M	probably damaging	Het
Btaf1	G	A	19: 36,994,857	V1331I	possibly damaging	Het
Ciz1	T	A	2: 32,376,043	I609K	possibly damaging	Het
Clca3b	C	T	3: 144,846,459	V154I	probably damaging	Het
Csde1	A	G	3: 103,052,841	T564A	possibly damaging	Het
Csrnp2	A	G	15: 100,482,054	V452A	probably benign	Het
Ctnnd1	C	T	2: 84,616,789	V371M	probably damaging	Het
Dock6	T	C	9: 21,832,881	D677G	probably damaging	Het
Filip1l	A	T	16: 57,570,255	E402V	probably damaging	Het
Gad1-ps	G	A	10: 99,445,147		noncoding transcript	Het
Ghr	G	A	15: 3,388,675	Q37*	probably null	Het
Gm10770	C	T	2: 150,179,423	R58H	probably benign	Het
Gm12789	T	C	4: 101,989,961	Y148H	possibly damaging	Het
Herc4	T	A	10: 63,275,013	N234K	probably benign	Het
Itih3	A	G	14: 30,923,521	V10A	probably benign	Het
Kat14	T	A	2: 144,393,323	D234E	probably benign	Het
Kif13a	A	G	13: 46,772,769		probably null	Het
Kif2b	A	G	11: 91,577,229	V76A	probably benign	Het
Mboat1	A	G	13: 30,219,667	T150A	probably benign	Het
Mfsd1	T	A	3: 67,599,960	L398H	probably damaging	Het
Myt1l	G	A	12: 29,832,332	G509R	unknown	Het
Nfx1	T	C	4: 41,004,343	C705R	probably damaging	Het
Olfr318	T	A	11: 58,720,524	N175Y	probably damaging	Het
Olfr60	A	G	7: 140,345,273	F239L	possibly damaging	Het
Pcdh10	T	C	3: 45,384,200	S931P	probably benign	Het
Pdpk1	T	C	17: 24,091,560	E205G	probably benign	Het
Ppp2r2a	A	T	14: 67,023,756	F172I	probably damaging	Het
Ppp2r5e	T	A	12: 75,453,763	D452V	probably damaging	Het
Rims2	A	T	15: 39,345,355	T185S	probably damaging	Het
Rpusd4	T	C	9: 35,272,602	V209A	probably benign	Het
Scaf8	C	A	17: 3,197,110	P903T	probably benign	Het
Slc30a7	A	G	3: 116,006,925	S31P	possibly damaging	Het
Slc9b1	T	C	3: 135,373,263		probably null	Het
Sntb1	C	G	15: 55,642,795	G461R	probably damaging	Het
Tbc1d32	T	C	10: 56,027,993	D1226G	probably damaging	Het
Tlnrd1	G	T	7: 83,882,314	T303N	probably damaging	Het
Tmc1	G	T	19: 20,789,622	N738K	possibly damaging	Het
Tmem41a	A	G	16: 21,934,856	I255T	probably benign	Het
Trim7	G	A	11: 48,849,955	C293Y	probably damaging	Het
Trpc6	C	T	9: 8,634,074	Q385*	probably null	Het
Ttc39b	A	G	4: 83,243,953	I330T	possibly damaging	Het
Vil1	C	T	1: 74,432,331	T757I	probably benign	Het
Zfp462	T	C	4: 55,060,077	V1201A	probably damaging	Het
Zfp473	T	A	7: 44,732,848	E686V	possibly damaging	Het

Other mutations in Safb

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01465:Safb	APN	17	56602974	unclassified	probably benign
IGL02391:Safb	APN	17	56600813	splice site	probably benign
IGL03145:Safb	APN	17	56605287	missense	probably damaging	1.00
R0245:Safb	UTSW	17	56606025	missense	probably damaging	1.00
R0464:Safb	UTSW	17	56606025	missense	probably damaging	1.00
R0468:Safb	UTSW	17	56606025	missense	probably damaging	1.00
R0479:Safb	UTSW	17	56606025	missense	probably damaging	1.00
R0496:Safb	UTSW	17	56605630	missense	probably benign	0.05
R0639:Safb	UTSW	17	56601092	utr 3 prime	probably benign
R0655:Safb	UTSW	17	56597803	missense	probably benign	0.23
R1109:Safb	UTSW	17	56601228	splice site	probably benign
R1941:Safb	UTSW	17	56598992	intron	probably benign
R1969:Safb	UTSW	17	56605821	missense	probably benign	0.32
R1971:Safb	UTSW	17	56605821	missense	probably benign	0.32
R4010:Safb	UTSW	17	56603765	unclassified	probably benign
R4132:Safb	UTSW	17	56600848	utr 3 prime	probably benign
R5681:Safb	UTSW	17	56599000	intron	probably benign
R5900:Safb	UTSW	17	56600349	missense	unknown
R6077:Safb	UTSW	17	56602956	unclassified	probably benign
R6173:Safb	UTSW	17	56597798	missense	probably damaging	1.00
R6367:Safb	UTSW	17	56593845	unclassified	probably benign
R6735:Safb	UTSW	17	56585169	unclassified	probably benign
R6736:Safb	UTSW	17	56606023	missense	possibly damaging	0.46
R7699:Safb	UTSW	17	56601504	missense	unknown
R7834:Safb	UTSW	17	56593881	missense	unknown
R7909:Safb	UTSW	17	56595665	missense	unknown
R8167:Safb	UTSW	17	56585286	missense	unknown
R8810:Safb	UTSW	17	56603579	missense	unknown
X0065:Safb	UTSW	17	56603798	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGCTGAGTTTCAATGCCCTG -3'
(R):5'- GCTCTGTTAGTACATGGGCC -3'

Sequencing Primer
(F):5'- GCTGAGTTTCAATGCCCTGAGAAC -3'
(R):5'- GGGCCTTATTTTCTGACAGACAAG -3'

Posted On

2016-09-01