Mutagenetix > Incidental Mutation

Incidental Mutation 'R0531:Sall4'

49141

Institutional Source

Beutler Lab

Gene Symbol

Sall4

Ensembl Gene

ENSMUSG00000027547

Gene Name

spalt like transcription factor 4

Synonyms

Tex20, 5730441M18Rik, C330011P20Rik

MMRRC Submission

038723-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0531 (G1)

Quality Score

176

Status

Validated

Chromosome

Chromosomal Location

168590252-168609121 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 168598256 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 195 (A195T)

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: A195T

PolyPhen 2 Score 0.096 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000029061
Gene: ENSMUSG00000027547
AA Change: A195T

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: A195T

PolyPhen 2 Score 0.096 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000099363
Gene: ENSMUSG00000027547
AA Change: A195T

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: A164T

PolyPhen 2 Score 0.046 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000115646
Gene: ENSMUSG00000027547
AA Change: A164T

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

0.0834

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.3%

Validation Efficiency

100% (69/69)

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930590J08Rik	A	G	6: 91,892,127 (GRCm39)	N130D	probably benign	Het
Acot6	C	A	12: 84,148,075 (GRCm39)	D110E	probably benign	Het
Agrn	T	A	4: 156,263,891 (GRCm39)	N124I	probably benign	Het
Astn1	G	T	1: 158,427,959 (GRCm39)	G710V	probably damaging	Het
Bcar3	T	C	3: 122,220,148 (GRCm39)	V15A	probably benign	Het
Best3	T	C	10: 116,840,280 (GRCm39)		probably benign	Het
Bltp1	T	A	3: 37,090,974 (GRCm39)	I743N	probably damaging	Het
Cenpa	T	C	5: 30,829,837 (GRCm39)	F39L	possibly damaging	Het
Cfap44	A	T	16: 44,221,789 (GRCm39)	M1L	probably benign	Het
Chrnd	A	G	1: 87,122,541 (GRCm39)	I107M	probably damaging	Het
Col11a2	A	G	17: 34,277,351 (GRCm39)		probably benign	Het
Dnah10	G	A	5: 124,889,787 (GRCm39)		probably null	Het
Entpd8	A	G	2: 24,974,781 (GRCm39)	Y404C	probably damaging	Het
Fam118a	T	C	15: 84,932,633 (GRCm39)	I125T	possibly damaging	Het
Fam161a	G	A	11: 22,970,298 (GRCm39)	E159K	possibly damaging	Het
Fkbp5	A	T	17: 28,657,003 (GRCm39)	H71Q	probably benign	Het
Frem2	A	T	3: 53,427,375 (GRCm39)	Y2926N	probably damaging	Het
Gap43	A	T	16: 42,112,691 (GRCm39)	D23E	probably damaging	Het
Glt8d1	T	C	14: 30,728,461 (GRCm39)	F3S	probably benign	Het
Gm11555	C	T	11: 99,540,844 (GRCm39)		probably benign	Het
Gtpbp1	G	A	15: 79,604,292 (GRCm39)	G667S	probably damaging	Het
H2-T24	A	C	17: 36,326,463 (GRCm39)	S145R	probably benign	Het
Inpp5b	A	T	4: 124,689,249 (GRCm39)	N843I	probably damaging	Het
Jak3	C	T	8: 72,139,620 (GRCm39)		probably benign	Het
Krt8	T	A	15: 101,909,883 (GRCm39)	M174L	probably benign	Het
Ktn1	C	T	14: 47,901,398 (GRCm39)	T52I	probably damaging	Het
Lrp4	T	C	2: 91,305,523 (GRCm39)		probably benign	Het
Nefh	G	A	11: 4,890,240 (GRCm39)	A793V	probably damaging	Het
Niban1	T	C	1: 151,593,835 (GRCm39)	V840A	probably benign	Het
Notch1	A	G	2: 26,356,584 (GRCm39)	S1678P	probably benign	Het
Notch2	C	T	3: 98,009,767 (GRCm39)		probably benign	Het
Nrxn3	T	C	12: 88,762,112 (GRCm39)	F53S	probably damaging	Het
Or10d4c	A	G	9: 39,558,168 (GRCm39)	T49A	probably benign	Het
Or2ab1	A	G	11: 58,488,674 (GRCm39)	I151V	probably benign	Het
Or5ac25	T	A	16: 59,182,171 (GRCm39)	N137Y	probably damaging	Het
Or6z5	A	T	7: 6,477,234 (GRCm39)	I42F	possibly damaging	Het
Or8g17	G	T	9: 38,930,472 (GRCm39)	R122S	probably damaging	Het
Or9i16	C	T	19: 13,865,116 (GRCm39)	V153I	possibly damaging	Het
Pak4	T	A	7: 28,267,479 (GRCm39)	I62F	possibly damaging	Het
Pcdhb12	T	A	18: 37,570,371 (GRCm39)	F506I	probably damaging	Het
Per1	A	T	11: 68,995,016 (GRCm39)	D632V	probably damaging	Het
Plec	A	G	15: 76,061,498 (GRCm39)	M2678T	probably benign	Het
Plg	A	G	17: 12,630,334 (GRCm39)		probably benign	Het
Prmt1	A	T	7: 44,627,048 (GRCm39)	S304R	probably damaging	Het
Prr27	T	C	5: 87,990,537 (GRCm39)	F50L	probably benign	Het
Prune2	T	C	19: 16,984,117 (GRCm39)	L159P	probably damaging	Het
Ptpn12	A	T	5: 21,203,481 (GRCm39)	N432K	possibly damaging	Het
Rfwd3	A	G	8: 112,020,621 (GRCm39)		probably null	Het
Rims2	A	T	15: 39,430,426 (GRCm39)	D1170V	probably damaging	Het
Sag	T	C	1: 87,762,351 (GRCm39)		probably null	Het
Sbf2	G	A	7: 109,966,530 (GRCm39)		probably benign	Het
Scaper	A	T	9: 55,517,158 (GRCm39)	D599E	possibly damaging	Het
Sema7a	G	A	9: 57,867,876 (GRCm39)	S484N	possibly damaging	Het
Senp1	A	G	15: 97,962,761 (GRCm39)		probably benign	Het
Senp6	A	G	9: 80,031,166 (GRCm39)	T623A	probably damaging	Het
Siae	A	G	9: 37,539,090 (GRCm39)	D95G	probably benign	Het
Slc26a2	T	C	18: 61,331,451 (GRCm39)	D660G	probably damaging	Het
Slc3a1	T	C	17: 85,336,077 (GRCm39)	F73S	possibly damaging	Het
Slfn5	A	T	11: 82,851,866 (GRCm39)	Q664L	probably damaging	Het
Spire1	T	C	18: 67,624,375 (GRCm39)	I512V	probably damaging	Het
Srpra	A	G	9: 35,124,797 (GRCm39)	T133A	probably benign	Het
Stag1	A	G	9: 100,836,300 (GRCm39)	*175W	probably null	Het
Stk32c	C	A	7: 138,700,636 (GRCm39)	V316F	probably damaging	Het
Tekt1	A	C	11: 72,236,420 (GRCm39)	N347K	possibly damaging	Het
Tmem81	C	G	1: 132,435,567 (GRCm39)	I124M	probably damaging	Het
Tnpo2	T	A	8: 85,776,786 (GRCm39)	C498S	probably damaging	Het
Tra2b	G	A	16: 22,065,955 (GRCm39)	R281*	probably null	Het
Ubr5	A	T	15: 37,991,588 (GRCm39)	I1985N	probably benign	Het
Ush2a	T	G	1: 188,175,378 (GRCm39)	S1159A	probably benign	Het
Vmn1r15	C	T	6: 57,235,236 (GRCm39)	P35S	probably benign	Het
Vmn1r6	A	T	6: 56,979,583 (GRCm39)	I60L	probably benign	Het
Vps8	A	G	16: 21,278,561 (GRCm39)		probably benign	Het
Xkr7	T	C	2: 152,874,272 (GRCm39)	V113A	possibly 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
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
R2067:Sall4	UTSW	2	168,598,465 (GRCm39)	missense	probably benign	0.00
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'- ACACGGACACTTGCTGAGACAC -3'
(R):5'- TCAGAGGACTTTTCCAGAGCTGCC -3'

Sequencing Primer
(F):5'- ACTTGCTGAGACACATGGC -3'
(R):5'- TTTCCAGAGCTGCCCTGAG -3'

Posted On

2013-06-12