Mutagenetix > Incidental Mutation

Incidental Mutation 'R2067:Sall4'

226733

Institutional Source

Beutler Lab

Gene Symbol

Sall4

Ensembl Gene

ENSMUSG00000027547

Gene Name

spalt like transcription factor 4

Synonyms

5730441M18Rik, Tex20, C330011P20Rik

MMRRC Submission

040072-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2067 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

168748332-168767943 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 168756545 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 125 (N125S)

Ref Sequence

ENSEMBL: ENSMUSP00000099363 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029061] [ENSMUST00000075044] [ENSMUST00000103074] [ENSMUST00000137536] [ENSMUST00000150588]

AlphaFold

Q8BX22

Predicted Effect

probably benign
Transcript: ENSMUST00000029061
AA Change: N125S

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000029061
Gene: ENSMUSG00000027547
AA Change: N125S

Domain	Start	End	E-Value	Type
low complexity region	15	24	N/A	INTRINSIC
low complexity region	25	42	N/A	INTRINSIC
ZnF_C2H2	68	88	1.31e2	SMART
low complexity region	193	203	N/A	INTRINSIC
low complexity region	210	230	N/A	INTRINSIC
low complexity region	254	278	N/A	INTRINSIC
low complexity region	295	313	N/A	INTRINSIC
ZnF_C2H2	387	409	1.04e-3	SMART
ZnF_C2H2	415	437	2.15e-5	SMART
ZnF_C2H2	573	595	5.34e0	SMART
ZnF_C2H2	601	623	1.22e-4	SMART
ZnF_C2H2	633	655	1.84e-4	SMART
low complexity region	855	867	N/A	INTRINSIC
ZnF_C2H2	880	902	2.53e-2	SMART
ZnF_C2H2	908	930	1.13e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000075044

SMART Domains

Protein: ENSMUSP00000074556
Gene: ENSMUSG00000027547

Domain	Start	End	E-Value	Type
low complexity region	15	24	N/A	INTRINSIC
low complexity region	30	38	N/A	INTRINSIC
low complexity region	66	78	N/A	INTRINSIC
ZnF_C2H2	91	113	2.53e-2	SMART
ZnF_C2H2	119	141	1.13e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000103074
AA Change: N125S

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000099363
Gene: ENSMUSG00000027547
AA Change: N125S

Domain	Start	End	E-Value	Type
low complexity region	15	24	N/A	INTRINSIC
low complexity region	25	42	N/A	INTRINSIC
ZnF_C2H2	68	88	1.31e2	SMART
low complexity region	193	203	N/A	INTRINSIC
low complexity region	210	230	N/A	INTRINSIC
low complexity region	254	278	N/A	INTRINSIC
low complexity region	295	313	N/A	INTRINSIC
low complexity region	411	423	N/A	INTRINSIC
ZnF_C2H2	436	458	2.53e-2	SMART
ZnF_C2H2	464	486	1.13e-4	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125138

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130640

Predicted Effect

probably benign
Transcript: ENSMUST00000137536
AA Change: N94S

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000115646
Gene: ENSMUSG00000027547
AA Change: N94S

Domain	Start	End	E-Value	Type
Blast:ZnF_C2H2	37	61	6e-9	BLAST
low complexity region	162	172	N/A	INTRINSIC
low complexity region	179	199	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000150588

SMART Domains

Protein: ENSMUSP00000119628
Gene: ENSMUSG00000027547

Domain	Start	End	E-Value	Type
ZnF_C2H2	64	86	1.22e-4	SMART
ZnF_C2H2	96	118	1.84e-4	SMART

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.5%
20x: 95.7%

Validation Efficiency

97% (76/78)

MGI Phenotype

FUNCTION: This gene belongs to the spalt family of zinc finger transcription factors. In mouse, functions for this gene have been described in many embryonic developmental processes, including brain, heart, and limb development. In addition, this gene is an important pluripotency factor that is required for stem cell maintenance. Homozygous mutant mice display embryonic lethality, while conditional knock-out in embryonic germ cells results in failure to establish a robust stem cell population. A pseudogene of this gene is found on chromosome 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
PHENOTYPE: Homozygous mutation of this gene results in early embryonic lethality before somite formation. Heterozygous mutation of this locus causes variable phenotypes, from heart and digit defects to deafness, anogenital tract defects, cranial and carpal bone defects and renal agenesis or hypoplasia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9530002B09Rik	T	A	4: 122,689,322		probably benign	Het
Abca2	A	T	2: 25,437,505	I669F	possibly damaging	Het
Acin1	T	A	14: 54,665,254	Q360H	probably damaging	Het
Aldh3b1	T	A	19: 3,921,755	D72V	probably benign	Het
Alox12e	G	A	11: 70,316,002	R620W	probably damaging	Het
Alpl	T	C	4: 137,749,545		probably benign	Het
Amy2a1	T	C	3: 113,530,568	I108V	probably benign	Het
Ascc2	A	T	11: 4,681,496	M646L	probably benign	Het
Bod1l	G	A	5: 41,817,086	T2295M	probably benign	Het
Ccdc9	A	T	7: 16,278,550		probably null	Het
Clptm1l	C	T	13: 73,607,723	Q153*	probably null	Het
Csmd1	A	G	8: 15,900,782	S3476P	probably benign	Het
Ddias	A	T	7: 92,859,699	M336K	possibly damaging	Het
Ehd1	T	C	19: 6,298,078	L362P	probably benign	Het
Epha1	G	T	6: 42,366,053	H187Q	probably benign	Het
Espl1	T	C	15: 102,299,090	S330P	probably damaging	Het
Fbln7	G	T	2: 128,877,466	R61L	probably damaging	Het
Fbxo41	C	T	6: 85,478,471	W577*	probably null	Het
Fgb	C	A	3: 83,049,689	D25Y	probably benign	Het
Gc	T	A	5: 89,446,517	K37N	probably damaging	Het
Gfpt1	T	C	6: 87,057,754	I178T	probably benign	Het
Gm12695	T	C	4: 96,769,726	T69A	probably benign	Het
Gm3944	C	A	12: 18,853,894	S8*	probably null	Het
Gm9912	T	C	3: 149,185,159	T113A	unknown	Het
Gpr156	A	G	16: 37,978,751	D109G	probably benign	Het
Hoxd1	A	T	2: 74,763,366	T89S	probably benign	Het
Htt	C	T	5: 34,825,982	T975I	probably benign	Het
Itpr3	G	A	17: 27,098,076	M768I	probably benign	Het
Krt4	C	A	15: 101,924,664	A3S	possibly damaging	Het
Mrto4	T	C	4: 139,349,023	K86E	probably benign	Het
Mup4	T	A	4: 59,960,622		probably benign	Het
Myh1	G	A	11: 67,214,620	D1079N	possibly damaging	Het
Myo1a	A	G	10: 127,705,478	N43D	probably benign	Het
Napa	A	T	7: 16,115,278		probably benign	Het
Ndufa12	A	G	10: 94,220,707	D99G	probably damaging	Het
Neb	A	G	2: 52,284,263	I1528T	probably benign	Het
Nek1	T	C	8: 61,007,162	S41P	probably damaging	Het
Nolc1	C	T	19: 46,083,607	T612M	probably damaging	Het
Nsun5	T	G	5: 135,375,072	Y301D	probably damaging	Het
Oas1g	T	C	5: 120,885,883	E121G	probably damaging	Het
Olfr1085	G	T	2: 86,658,437	T7K	probably damaging	Het
Olfr1170	A	G	2: 88,224,474	V186A	possibly damaging	Het
Olfr324	A	G	11: 58,597,570	N58S	probably damaging	Het
Olfr397	A	G	11: 73,964,914	Y102C	probably damaging	Het
Olfr522	T	A	7: 140,162,909	I14F	possibly damaging	Het
Olfr910	T	A	9: 38,539,280	N128K	probably benign	Het
Osmr	T	C	15: 6,815,415	N957D	probably benign	Het
Parn	G	A	16: 13,603,069	S473L	probably damaging	Het
Phc2	T	C	4: 128,747,136	F672S	probably damaging	Het
Pik3c2b	T	C	1: 133,099,611	S1283P	probably damaging	Het
Pole2	G	A	12: 69,228,152	R5W	probably benign	Het
Prl7a2	T	A	13: 27,660,887	Y172F	probably damaging	Het
Ptprz1	A	G	6: 23,050,389		probably benign	Het
Rapgef3	C	A	15: 97,766,961	G7V	probably damaging	Het
Ripor1	T	A	8: 105,617,708	S491R	probably benign	Het
Rnf141	A	G	7: 110,821,365		probably benign	Het
Ryr3	C	T	2: 112,946,957	R285Q	probably damaging	Het
Schip1	A	G	3: 68,617,786	K360R	probably damaging	Het
Senp6	T	A	9: 80,089,869	V55E	probably benign	Het
Skint1	T	A	4: 112,025,533	V258D	probably benign	Het
Slc25a16	T	A	10: 62,932,751	H130Q	probably benign	Het
Styx	T	C	14: 45,373,563	V217A	probably benign	Het
Syne2	G	A	12: 75,888,342		probably null	Het
Tagap1	A	G	17: 6,956,860	S146P	probably benign	Het
Tatdn2	A	G	6: 113,704,142	K379E	probably benign	Het
Thrap3	T	C	4: 126,175,396	Y654C	possibly damaging	Het
Tle2	T	C	10: 81,580,551	L135P	probably damaging	Het
Tmc1	A	G	19: 20,824,309	F451S	possibly damaging	Het
Trpm7	G	A	2: 126,797,727	P1650S	probably damaging	Het
Ttll4	G	A	1: 74,680,382	R16H	possibly damaging	Het
Ttn	T	C	2: 76,714,373	N32795S	probably damaging	Het
Tubgcp6	T	C	15: 89,104,489	E803G	probably benign	Het
Ubr2	A	G	17: 46,963,145		probably null	Het
Ugt2b35	A	G	5: 87,001,553	D221G	probably damaging	Het
Unc45b	G	A	11: 82,911,689	A4T	probably benign	Het
Vmn1r70	A	T	7: 10,634,337	I251F	possibly damaging	Het
Vmn2r120	T	A	17: 57,524,553	H412L	possibly damaging	Het
Zfp59	A	G	7: 27,853,510	N129S	probably benign	Het
Zgrf1	T	C	3: 127,613,350	C1589R	probably damaging	Het

Other mutations in Sall4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00569:Sall4	APN	2	168755312	missense	probably benign	0.02
IGL00592:Sall4	APN	2	168755963	missense	probably damaging	1.00
IGL00674:Sall4	APN	2	168755780	missense	probably damaging	0.99
IGL01308:Sall4	APN	2	168750244	missense	probably damaging	0.99
IGL01538:Sall4	APN	2	168755856	missense	probably damaging	1.00
IGL01552:Sall4	APN	2	168756123	missense	probably damaging	1.00
IGL02614:Sall4	APN	2	168755885	missense	probably null	0.79
R0514:Sall4	UTSW	2	168755705	missense	probably damaging	1.00
R0531:Sall4	UTSW	2	168756336	missense	probably benign	0.10
R0747:Sall4	UTSW	2	168754966	missense	probably damaging	1.00
R1371:Sall4	UTSW	2	168756474	missense	probably benign	0.10
R1736:Sall4	UTSW	2	168752635	missense	probably benign	0.10
R3766:Sall4	UTSW	2	168756044	missense	possibly damaging	0.93
R3783:Sall4	UTSW	2	168756123	missense	probably damaging	1.00
R3784:Sall4	UTSW	2	168756123	missense	probably damaging	1.00
R3785:Sall4	UTSW	2	168756123	missense	probably damaging	1.00
R3787:Sall4	UTSW	2	168756123	missense	probably damaging	1.00
R3877:Sall4	UTSW	2	168756242	missense	probably damaging	1.00
R4356:Sall4	UTSW	2	168755480	missense	probably benign	0.37
R4358:Sall4	UTSW	2	168755480	missense	probably benign	0.37
R4760:Sall4	UTSW	2	168750427	missense	probably damaging	0.98
R4869:Sall4	UTSW	2	168755717	missense	probably damaging	1.00
R5979:Sall4	UTSW	2	168750343	missense	probably benign	0.28
R6089:Sall4	UTSW	2	168755486	missense	possibly damaging	0.92
R6502:Sall4	UTSW	2	168755708	missense	probably damaging	1.00
R6990:Sall4	UTSW	2	168755070	missense	probably damaging	1.00
R7999:Sall4	UTSW	2	168752641	missense	probably damaging	0.99
R8436:Sall4	UTSW	2	168755910	missense	probably damaging	1.00
R9069:Sall4	UTSW	2	168754853	missense	probably benign	0.00
R9375:Sall4	UTSW	2	168755861	missense	probably damaging	0.99
R9630:Sall4	UTSW	2	168754488	missense	probably benign
R9720:Sall4	UTSW	2	168750240	missense	probably damaging	1.00
Z1177:Sall4	UTSW	2	168752575	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CGCGAATCTGTTCCGTAAGC -3'
(R):5'- GGAGGACACTCACATCTGCAAC -3'

Sequencing Primer
(F):5'- GATCTGCTCCAGGACCCAAG -3'
(R):5'- ACAAATGCTGTGCCGAGTTC -3'

Posted On

2014-09-17