Mutagenetix > Incidental Mutation

Incidental Mutation 'R4760:Sall4'

356777

Institutional Source

Beutler Lab

Gene Symbol

Sall4

Ensembl Gene

ENSMUSG00000027547

Gene Name

spalt like transcription factor 4

Synonyms

Tex20, 5730441M18Rik, C330011P20Rik

MMRRC Submission

041974-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4760 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

168590252-168609121 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 168592347 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 936 (S936P)

Ref Sequence

ENSEMBL: ENSMUSP00000029061 (fasta)

Gene Model

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

AlphaFold

Q8BX22

Predicted Effect

probably damaging
Transcript: ENSMUST00000029061
AA Change: S936P

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000029061
Gene: ENSMUSG00000027547
AA Change: S936P

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
AA Change: S147P

PolyPhen 2 Score 0.123 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000074556
Gene: ENSMUSG00000027547
AA Change: S147P

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: S492P

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000099363
Gene: ENSMUSG00000027547
AA Change: S492P

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

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

0.1737

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.9%
20x: 94.4%

Validation Efficiency

98% (90/92)

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A530053G22Rik	A	G	6: 60,379,086 (GRCm39)		noncoding transcript	Het
Abcc2	A	T	19: 43,798,920 (GRCm39)	Y512F	probably benign	Het
Adgrb1	T	A	15: 74,443,312 (GRCm39)	I51N	probably damaging	Het
Adhfe1	A	G	1: 9,633,748 (GRCm39)	Y332C	probably damaging	Het
Ambn	C	T	5: 88,615,566 (GRCm39)	L317F	probably damaging	Het
Amn1	T	C	6: 149,086,611 (GRCm39)	Y17C	probably benign	Het
Apoa5	T	C	9: 46,181,593 (GRCm39)	V223A	probably damaging	Het
Best3	A	T	10: 116,860,699 (GRCm39)	H653L	probably benign	Het
Btnl2	C	A	17: 34,582,169 (GRCm39)	S245Y	probably damaging	Het
Camk1d	A	G	2: 5,366,867 (GRCm39)	L116P	probably damaging	Het
Catsperg2	T	A	7: 29,405,060 (GRCm39)	D698V	probably damaging	Het
Cd33	T	C	7: 43,178,919 (GRCm39)	T307A	probably benign	Het
Cdk8	C	T	5: 146,229,476 (GRCm39)	S230L	probably benign	Het
Cfap69	C	T	5: 5,696,939 (GRCm39)	C119Y	probably damaging	Het
Chat	T	C	14: 32,175,694 (GRCm39)	N122S	probably benign	Het
Col20a1	A	T	2: 180,626,196 (GRCm39)		probably benign	Het
Cyp2j9	A	T	4: 96,457,028 (GRCm39)	L481Q	probably damaging	Het
Dab1	A	C	4: 104,589,342 (GRCm39)	S550R	probably damaging	Het
Dlgap2	A	C	8: 14,823,380 (GRCm39)	Q533P	probably damaging	Het
Eif4g3	A	T	4: 137,811,629 (GRCm39)	Q31L	possibly damaging	Het
Ets2	G	A	16: 95,520,087 (GRCm39)	V438M	probably damaging	Het
Eva1c	G	A	16: 90,701,138 (GRCm39)	D258N	probably benign	Het
Fastkd2	A	G	1: 63,785,045 (GRCm39)	H477R	probably benign	Het
Fga	T	G	3: 82,938,821 (GRCm39)	S399A	probably benign	Het
Fmo4	T	A	1: 162,637,396 (GRCm39)	E32V	probably damaging	Het
Gm7204	T	A	16: 48,039,051 (GRCm39)		noncoding transcript	Het
Gpi-ps	G	A	8: 5,690,473 (GRCm39)		noncoding transcript	Het
Hhipl1	A	G	12: 108,286,336 (GRCm39)	I548V	probably damaging	Het
Hsfy2	T	C	1: 56,676,349 (GRCm39)	T63A	probably benign	Het
Igf2r	A	G	17: 12,922,352 (GRCm39)	V1254A	possibly damaging	Het
Ighv8-4	A	T	12: 114,987,667 (GRCm39)	D110E	probably damaging	Het
Igkv14-130	T	C	6: 67,768,446 (GRCm39)	S101P	probably benign	Het
Igkv9-120	G	T	6: 68,027,351 (GRCm39)	R88S	possibly damaging	Het
Ipo5	T	C	14: 121,179,054 (GRCm39)	V779A	probably benign	Het
Itpr1	C	T	6: 108,326,593 (GRCm39)	T105I	probably benign	Het
Kalrn	T	C	16: 34,018,857 (GRCm39)	M670V	probably damaging	Het
Kdm8	T	A	7: 125,054,431 (GRCm39)		probably null	Het
Kics2	T	C	10: 121,575,912 (GRCm39)	V11A	probably damaging	Het
L3hypdh	T	C	12: 72,124,016 (GRCm39)	I281V	probably benign	Het
Lins1	T	G	7: 66,364,435 (GRCm39)		probably benign	Het
Map4k5	T	A	12: 69,871,372 (GRCm39)	I517L	possibly damaging	Het
Marchf2	G	T	17: 33,928,890 (GRCm39)	T2K	probably damaging	Het
Mlkl	C	G	8: 112,046,348 (GRCm39)		probably null	Het
Mllt1	A	G	17: 57,209,630 (GRCm39)	M160T	probably benign	Het
Mmp15	G	A	8: 96,094,824 (GRCm39)	A233T	possibly damaging	Het
Moxd2	C	A	6: 40,868,537 (GRCm39)	T23N	probably benign	Het
Nop53	C	A	7: 15,676,812 (GRCm39)	K100N	probably benign	Het
Nrg1	C	A	8: 32,408,228 (GRCm39)	E2*	probably null	Het
Or52u1	T	A	7: 104,237,696 (GRCm39)	H228Q	probably benign	Het
Pank4	A	G	4: 155,059,091 (GRCm39)	D408G	possibly damaging	Het
Pcdhb10	T	C	18: 37,544,995 (GRCm39)	W24R	probably benign	Het
Pcm1	C	T	8: 41,740,775 (GRCm39)	T968I	probably damaging	Het
Pkib	G	T	10: 57,584,246 (GRCm39)	M19I	probably benign	Het
Ppy	A	G	11: 101,991,345 (GRCm39)		probably null	Het
Pramel21	G	A	4: 143,343,801 (GRCm39)	R367K	probably benign	Het
Prdx3	A	C	19: 60,861,621 (GRCm39)	C39W	possibly damaging	Het
Qrfpr	T	G	3: 36,276,073 (GRCm39)	N106H	probably benign	Het
Rai14	G	A	15: 10,575,776 (GRCm39)	T394M	possibly damaging	Het
Ralgapa2	A	T	2: 146,188,669 (GRCm39)	L1371Q	probably benign	Het
Rbm12	A	G	2: 155,939,048 (GRCm39)	L408P	probably damaging	Het
Rdx	T	C	9: 51,977,174 (GRCm39)	I141T	probably benign	Het
Reep1	T	A	6: 71,684,985 (GRCm39)	V11E	possibly damaging	Het
Relch	T	A	1: 105,649,030 (GRCm39)	M723K	probably benign	Het
Serac1	A	G	17: 6,102,065 (GRCm39)	M403T	possibly damaging	Het
Shroom3	G	T	5: 93,090,945 (GRCm39)	V1151F	probably damaging	Het
Slc35g2	T	G	9: 100,435,549 (GRCm39)	I41L	probably benign	Het
Slc39a12	G	A	2: 14,405,134 (GRCm39)	S242N	probably benign	Het
Slc9a2	T	A	1: 40,801,076 (GRCm39)	D535E	probably damaging	Het
Spata31d1a	G	T	13: 59,849,459 (GRCm39)	P890T	probably damaging	Het
Sync	A	G	4: 129,187,232 (GRCm39)	Q88R	probably benign	Het
Tdrp	A	G	8: 14,024,527 (GRCm39)		probably benign	Het
Tg	G	T	15: 66,565,168 (GRCm39)	C1170F	probably damaging	Het
Tnks	A	T	8: 35,318,937 (GRCm39)	D781E	probably benign	Het
Tnp2	T	A	16: 10,606,207 (GRCm39)	T87S	possibly damaging	Het
Tpp2	T	C	1: 44,010,875 (GRCm39)	V554A	probably benign	Het
Traf3ip2	T	C	10: 39,521,735 (GRCm39)	I431T	probably damaging	Het
Trav9d-4	A	T	14: 53,221,258 (GRCm39)	H84L	probably damaging	Het
Vmn2r42	T	A	7: 8,187,276 (GRCm39)	Y782F	probably damaging	Het
Vwf	T	C	6: 125,547,567 (GRCm39)	S231P	probably damaging	Het
Wdr83os	A	G	8: 85,808,496 (GRCm39)	S83G	probably damaging	Het
Wdr91	T	A	6: 34,885,234 (GRCm39)	Q109L	probably damaging	Het
Znrf4	A	G	17: 56,818,864 (GRCm39)	C148R	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
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
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
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'- GATCTCGTTGGTCTTCATGGCC -3'
(R):5'- CACAAGCATGCTCTCAACTG -3'

Sequencing Primer
(F):5'- GTCTTCATGGCCAGACCC -3'
(R):5'- CTGGCTTACTGATACAAGATCTGAC -3'

Posted On

2015-11-11