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

Tex20, 5730441M18Rik, 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

168590252-168609121 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 168598465 bp (GRCm39)

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: 122,583,115 (GRCm39)		probably benign	Het
Abca2	A	T	2: 25,327,517 (GRCm39)	I669F	possibly damaging	Het
Acin1	T	A	14: 54,902,711 (GRCm39)	Q360H	probably damaging	Het
Aldh3b1	T	A	19: 3,971,755 (GRCm39)	D72V	probably benign	Het
Alox12e	G	A	11: 70,206,828 (GRCm39)	R620W	probably damaging	Het
Alpl	T	C	4: 137,476,856 (GRCm39)		probably benign	Het
Amy2a1	T	C	3: 113,324,217 (GRCm39)	I108V	probably benign	Het
Ascc2	A	T	11: 4,631,496 (GRCm39)	M646L	probably benign	Het
Bod1l	G	A	5: 41,974,429 (GRCm39)	T2295M	probably benign	Het
Ccdc9	A	T	7: 16,012,475 (GRCm39)		probably null	Het
Clptm1l	C	T	13: 73,755,842 (GRCm39)	Q153*	probably null	Het
Csmd1	A	G	8: 15,950,782 (GRCm39)	S3476P	probably benign	Het
Ddias	A	T	7: 92,508,907 (GRCm39)	M336K	possibly damaging	Het
Ehd1	T	C	19: 6,348,108 (GRCm39)	L362P	probably benign	Het
Epha1	G	T	6: 42,342,987 (GRCm39)	H187Q	probably benign	Het
Espl1	T	C	15: 102,207,525 (GRCm39)	S330P	probably damaging	Het
Fbln7	G	T	2: 128,719,386 (GRCm39)	R61L	probably damaging	Het
Fbxo41	C	T	6: 85,455,453 (GRCm39)	W577*	probably null	Het
Fgb	C	A	3: 82,956,996 (GRCm39)	D25Y	probably benign	Het
Gc	T	A	5: 89,594,376 (GRCm39)	K37N	probably damaging	Het
Gfpt1	T	C	6: 87,034,736 (GRCm39)	I178T	probably benign	Het
Gm12695	T	C	4: 96,657,963 (GRCm39)	T69A	probably benign	Het
Gm3944	C	A	12: 18,903,895 (GRCm39)	S8*	probably null	Het
Gm9912	T	C	3: 148,890,795 (GRCm39)	T113A	unknown	Het
Gpr156	A	G	16: 37,799,113 (GRCm39)	D109G	probably benign	Het
Hoxd1	A	T	2: 74,593,710 (GRCm39)	T89S	probably benign	Het
Htt	C	T	5: 34,983,326 (GRCm39)	T975I	probably benign	Het
Itpr3	G	A	17: 27,317,050 (GRCm39)	M768I	probably benign	Het
Krt4	C	A	15: 101,833,099 (GRCm39)	A3S	possibly damaging	Het
Mrto4	T	C	4: 139,076,334 (GRCm39)	K86E	probably benign	Het
Mup4	T	A	4: 59,960,622 (GRCm39)		probably benign	Het
Myh1	G	A	11: 67,105,446 (GRCm39)	D1079N	possibly damaging	Het
Myo1a	A	G	10: 127,541,347 (GRCm39)	N43D	probably benign	Het
Napa	A	T	7: 15,849,203 (GRCm39)		probably benign	Het
Ndufa12	A	G	10: 94,056,569 (GRCm39)	D99G	probably damaging	Het
Neb	A	G	2: 52,174,275 (GRCm39)	I1528T	probably benign	Het
Nek1	T	C	8: 61,460,196 (GRCm39)	S41P	probably damaging	Het
Nolc1	C	T	19: 46,072,046 (GRCm39)	T612M	probably damaging	Het
Nsun5	T	G	5: 135,403,926 (GRCm39)	Y301D	probably damaging	Het
Oas1g	T	C	5: 121,023,946 (GRCm39)	E121G	probably damaging	Het
Or1e1f	A	G	11: 73,855,740 (GRCm39)	Y102C	probably damaging	Het
Or2ab1	A	G	11: 58,488,396 (GRCm39)	N58S	probably damaging	Het
Or5d41	A	G	2: 88,054,818 (GRCm39)	V186A	possibly damaging	Het
Or6ae1	T	A	7: 139,742,822 (GRCm39)	I14F	possibly damaging	Het
Or8b46	T	A	9: 38,450,576 (GRCm39)	N128K	probably benign	Het
Or8k38	G	T	2: 86,488,781 (GRCm39)	T7K	probably damaging	Het
Osmr	T	C	15: 6,844,896 (GRCm39)	N957D	probably benign	Het
Parn	G	A	16: 13,420,933 (GRCm39)	S473L	probably damaging	Het
Phc2	T	C	4: 128,640,929 (GRCm39)	F672S	probably damaging	Het
Pik3c2b	T	C	1: 133,027,349 (GRCm39)	S1283P	probably damaging	Het
Pole2	G	A	12: 69,274,926 (GRCm39)	R5W	probably benign	Het
Prl7a2	T	A	13: 27,844,870 (GRCm39)	Y172F	probably damaging	Het
Ptprz1	A	G	6: 23,050,388 (GRCm39)		probably benign	Het
Rapgef3	C	A	15: 97,664,842 (GRCm39)	G7V	probably damaging	Het
Ripor1	T	A	8: 106,344,340 (GRCm39)	S491R	probably benign	Het
Rnf141	A	G	7: 110,420,572 (GRCm39)		probably benign	Het
Ryr3	C	T	2: 112,777,302 (GRCm39)	R285Q	probably damaging	Het
Schip1	A	G	3: 68,525,119 (GRCm39)	K360R	probably damaging	Het
Senp6	T	A	9: 79,997,151 (GRCm39)	V55E	probably benign	Het
Skint1	T	A	4: 111,882,730 (GRCm39)	V258D	probably benign	Het
Slc25a16	T	A	10: 62,768,530 (GRCm39)	H130Q	probably benign	Het
Styx	T	C	14: 45,611,020 (GRCm39)	V217A	probably benign	Het
Syne2	G	A	12: 75,935,116 (GRCm39)		probably null	Het
Tagap1	A	G	17: 7,224,259 (GRCm39)	S146P	probably benign	Het
Tatdn2	A	G	6: 113,681,103 (GRCm39)	K379E	probably benign	Het
Thrap3	T	C	4: 126,069,189 (GRCm39)	Y654C	possibly damaging	Het
Tle2	T	C	10: 81,416,385 (GRCm39)	L135P	probably damaging	Het
Tmc1	A	G	19: 20,801,673 (GRCm39)	F451S	possibly damaging	Het
Trpm7	G	A	2: 126,639,647 (GRCm39)	P1650S	probably damaging	Het
Ttll4	G	A	1: 74,719,541 (GRCm39)	R16H	possibly damaging	Het
Ttn	T	C	2: 76,544,717 (GRCm39)	N32795S	probably damaging	Het
Tubgcp6	T	C	15: 88,988,692 (GRCm39)	E803G	probably benign	Het
Ubr2	A	G	17: 47,274,071 (GRCm39)		probably null	Het
Ugt2b35	A	G	5: 87,149,412 (GRCm39)	D221G	probably damaging	Het
Unc45b	G	A	11: 82,802,515 (GRCm39)	A4T	probably benign	Het
Vmn1r70	A	T	7: 10,368,264 (GRCm39)	I251F	possibly damaging	Het
Vmn2r120	T	A	17: 57,831,553 (GRCm39)	H412L	possibly damaging	Het
Zfp59	A	G	7: 27,552,935 (GRCm39)	N129S	probably benign	Het
Zgrf1	T	C	3: 127,406,999 (GRCm39)	C1589R	probably damaging	Het

Other mutations in Sall4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00569:Sall4	APN	2	168,597,232 (GRCm39)	missense	probably benign	0.02
IGL00592:Sall4	APN	2	168,597,883 (GRCm39)	missense	probably damaging	1.00
IGL00674:Sall4	APN	2	168,597,700 (GRCm39)	missense	probably damaging	0.99
IGL01308:Sall4	APN	2	168,592,164 (GRCm39)	missense	probably damaging	0.99
IGL01538:Sall4	APN	2	168,597,776 (GRCm39)	missense	probably damaging	1.00
IGL01552:Sall4	APN	2	168,598,043 (GRCm39)	missense	probably damaging	1.00
IGL02614:Sall4	APN	2	168,597,805 (GRCm39)	missense	probably null	0.79
R0514:Sall4	UTSW	2	168,597,625 (GRCm39)	missense	probably damaging	1.00
R0531:Sall4	UTSW	2	168,598,256 (GRCm39)	missense	probably benign	0.10
R0747:Sall4	UTSW	2	168,596,886 (GRCm39)	missense	probably damaging	1.00
R1371:Sall4	UTSW	2	168,598,394 (GRCm39)	missense	probably benign	0.10
R1736:Sall4	UTSW	2	168,594,555 (GRCm39)	missense	probably benign	0.10
R3766:Sall4	UTSW	2	168,597,964 (GRCm39)	missense	possibly damaging	0.93
R3783:Sall4	UTSW	2	168,598,043 (GRCm39)	missense	probably damaging	1.00
R3784:Sall4	UTSW	2	168,598,043 (GRCm39)	missense	probably damaging	1.00
R3785:Sall4	UTSW	2	168,598,043 (GRCm39)	missense	probably damaging	1.00
R3787:Sall4	UTSW	2	168,598,043 (GRCm39)	missense	probably damaging	1.00
R3877:Sall4	UTSW	2	168,598,162 (GRCm39)	missense	probably damaging	1.00
R4356:Sall4	UTSW	2	168,597,400 (GRCm39)	missense	probably benign	0.37
R4358:Sall4	UTSW	2	168,597,400 (GRCm39)	missense	probably benign	0.37
R4760:Sall4	UTSW	2	168,592,347 (GRCm39)	missense	probably damaging	0.98
R4869:Sall4	UTSW	2	168,597,637 (GRCm39)	missense	probably damaging	1.00
R5979:Sall4	UTSW	2	168,592,263 (GRCm39)	missense	probably benign	0.28
R6089:Sall4	UTSW	2	168,597,406 (GRCm39)	missense	possibly damaging	0.92
R6502:Sall4	UTSW	2	168,597,628 (GRCm39)	missense	probably damaging	1.00
R6990:Sall4	UTSW	2	168,596,990 (GRCm39)	missense	probably damaging	1.00
R7999:Sall4	UTSW	2	168,594,561 (GRCm39)	missense	probably damaging	0.99
R8436:Sall4	UTSW	2	168,597,830 (GRCm39)	missense	probably damaging	1.00
R9069:Sall4	UTSW	2	168,596,773 (GRCm39)	missense	probably benign	0.00
R9375:Sall4	UTSW	2	168,597,781 (GRCm39)	missense	probably damaging	0.99
R9630:Sall4	UTSW	2	168,596,408 (GRCm39)	missense	probably benign
R9720:Sall4	UTSW	2	168,592,160 (GRCm39)	missense	probably damaging	1.00
Z1177:Sall4	UTSW	2	168,594,495 (GRCm39)	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