Mutagenetix > Incidental Mutation

Incidental Mutation 'R8889:Sox2'

677539

Institutional Source

Beutler Lab

Gene Symbol

Sox2

Ensembl Gene

ENSMUSG00000074637

Gene Name

SRY (sex determining region Y)-box 2

Synonyms

Sox-2, lcc, ysb

MMRRC Submission

068693-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8889 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

34704554-34706610 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 34705129 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Tyrosine at position 189 (N189Y)

Ref Sequence

ENSEMBL: ENSMUSP00000096755 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000099151]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000099151
AA Change: N189Y

PolyPhen 2 Score 0.658 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000096755
Gene: ENSMUSG00000074637
AA Change: N189Y

Domain	Start	End	E-Value	Type
low complexity region	19	35	N/A	INTRINSIC
HMG	42	112	1.8e-28	SMART
low complexity region	137	156	N/A	INTRINSIC
low complexity region	248	263	N/A	INTRINSIC

Meta Mutation Damage Score

0.2885

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (78/78)

MGI Phenotype

FUNCTION: This intronless gene encodes a member of the SRY-related HMG-box (SOX) family of transcription factors involved in the regulation of embryonic development and in the determination of cell fate. The product of this gene is required for stem-cell maintenance in the central nervous system, and also regulates gene expression in the stomach. Mutations in a similar gene in human have been associated with optic nerve hypoplasia and with syndromic microphthalmia, a severe form of structural eye malformation. This gene lies within an intron of another gene called SOX2 overlapping transcript (Sox2ot). [provided by RefSeq, Sep 2015]
PHENOTYPE: Homozygotes for targeted null mutations implant but fail to develop an egg cylinder or epiblast, and die shortly thereafter. Other mutations that affect only regulatory elements show circling behavior and deafness, inner ear defects, and a yellow coat color. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca14	T	A	7: 119,815,606 (GRCm39)	L285I	probably damaging	Het
Abcc2	T	G	19: 43,795,571 (GRCm39)	S442R	possibly damaging	Het
Adgrl3	A	T	5: 81,874,516 (GRCm39)	I938F	probably damaging	Het
Ank1	T	C	8: 23,606,990 (GRCm39)	L1297P	probably damaging	Het
Ap3b1	G	A	13: 94,679,348 (GRCm39)	V997M	unknown	Het
Ash2l	T	C	8: 26,313,247 (GRCm39)	K413R	probably benign	Het
Cacnb1	A	T	11: 97,901,192 (GRCm39)	V220E	probably damaging	Het
Cacul1	A	T	19: 60,568,960 (GRCm39)	L66Q	probably damaging	Het
Camkv	C	T	9: 107,823,333 (GRCm39)	R120*	probably null	Het
Ccny	T	G	18: 9,345,235 (GRCm39)	S180R	probably damaging	Het
Cdh23	G	T	10: 60,143,284 (GRCm39)	H3012Q	probably damaging	Het
Clasp2	T	A	9: 113,709,251 (GRCm39)	L680Q	probably damaging	Het
Clip1	A	T	5: 123,717,565 (GRCm39)	S1241R	probably benign	Het
Cthrc1	T	A	15: 38,940,445 (GRCm39)	L16H	probably damaging	Het
Ctnna1	G	A	18: 35,372,586 (GRCm39)	V514I	possibly damaging	Het
Ddr1	A	C	17: 35,993,556 (GRCm39)	I852S	probably benign	Het
Echs1	A	C	7: 139,688,031 (GRCm39)	L258R	probably damaging	Het
Epha8	G	T	4: 136,661,850 (GRCm39)	H582N	probably benign	Het
Exph5	G	T	9: 53,287,955 (GRCm39)	G1679W	probably damaging	Het
Fhod3	G	A	18: 25,189,452 (GRCm39)		probably null	Het
Gm10803	G	A	2: 93,394,281 (GRCm39)	D18N	unknown	Het
Gpr152	T	A	19: 4,192,723 (GRCm39)	I88N	probably damaging	Het
Gpr179	T	C	11: 97,226,590 (GRCm39)	D1855G	possibly damaging	Het
H2al2a	T	A	2: 18,001,599 (GRCm39)	D29V	probably damaging	Het
Hnrnpf	T	G	6: 117,901,753 (GRCm39)	S346A	probably benign	Het
Hsd11b2	C	T	8: 106,249,263 (GRCm39)	R213C	probably damaging	Het
Il17rd	A	G	14: 26,821,930 (GRCm39)	D552G	possibly damaging	Het
Ipo9	T	C	1: 135,314,544 (GRCm39)	N904S	possibly damaging	Het
Klhl14	T	G	18: 21,691,220 (GRCm39)	T437P	possibly damaging	Het
Krt5	T	C	15: 101,619,185 (GRCm39)	M268V	probably benign	Het
Lhx4	T	C	1: 155,581,013 (GRCm39)	T171A	possibly damaging	Het
Ltn1	A	T	16: 87,229,230 (GRCm39)		probably benign	Het
Macf1	A	G	4: 123,249,036 (GRCm39)	L7165P	probably damaging	Het
Micall2	T	A	5: 139,703,254 (GRCm39)	H194L	probably damaging	Het
Mmp16	T	A	4: 18,051,820 (GRCm39)	Y270N	probably damaging	Het
Nme6	T	G	9: 109,668,706 (GRCm39)	F41V	probably damaging	Het
Npffr1	A	G	10: 61,449,939 (GRCm39)	N71S	possibly damaging	Het
Or1p4-ps1	T	C	11: 74,207,949 (GRCm39)	W33R	probably damaging	Het
Or4k41	A	G	2: 111,279,967 (GRCm39)	I161V	probably benign	Het
Pard3b	T	A	1: 62,677,026 (GRCm39)	Y1186N	probably damaging	Het
Pate5	T	A	9: 35,750,682 (GRCm39)	T47S	probably damaging	Het
Pcca	A	G	14: 122,795,123 (GRCm39)		probably benign	Het
Plekha8	A	G	6: 54,592,540 (GRCm39)		probably benign	Het
Ptpn14	T	A	1: 189,554,872 (GRCm39)	L144*	probably null	Het
Rad52	C	T	6: 119,890,041 (GRCm39)	R56C	probably damaging	Het
Rdx	C	T	9: 51,997,753 (GRCm39)	R576C	probably damaging	Het
Rnf135	C	T	11: 80,074,957 (GRCm39)	T72I	probably benign	Het
Robo4	G	T	9: 37,314,601 (GRCm39)	R196L	probably benign	Het
Rsf1	G	GACGTCGGCT	7: 97,229,116 (GRCm39)		probably benign	Het
Rsf1	A	T	7: 97,328,171 (GRCm39)	I1058F		Het
Ryr2	A	T	13: 11,799,990 (GRCm39)	V919E	probably damaging	Het
Slc39a6	A	T	18: 24,729,386 (GRCm39)	Y442*	probably null	Het
Slc4a11	T	G	2: 130,529,140 (GRCm39)	S437R	probably damaging	Het
Slc7a6	T	A	8: 106,922,534 (GRCm39)	V440E	probably damaging	Het
Spata13	A	T	14: 60,994,030 (GRCm39)	M1161L	probably benign	Het
Spock3	T	A	8: 63,404,986 (GRCm39)	Y51*	probably null	Het
Sptbn1	A	G	11: 30,067,800 (GRCm39)	Y1805H	probably benign	Het
Tcerg1l	C	T	7: 137,999,260 (GRCm39)	W41*	probably null	Het
Tdrd9	A	G	12: 111,979,718 (GRCm39)	Y401C	probably benign	Het
Tex47	A	T	5: 7,355,115 (GRCm39)	I99F	probably damaging	Het
Tlr9	G	A	9: 106,099,834 (GRCm39)		probably benign	Het
Tmem209	T	A	6: 30,497,942 (GRCm39)	S276C	possibly damaging	Het
Tmprss11f	A	C	5: 86,687,618 (GRCm39)	S97A	possibly damaging	Het
Tnfaip8	ACACACTC	AC	18: 50,179,908 (GRCm39)		probably benign	Het
Ttc7	T	A	17: 87,637,520 (GRCm39)	M425K	probably damaging	Het
Ttn	C	T	2: 76,739,466 (GRCm39)	G3737D	unknown	Het
Unc13b	A	T	4: 43,176,484 (GRCm39)	R2437S	unknown	Het
Uqcrc1	C	T	9: 108,766,186 (GRCm39)	R58C	probably damaging	Het
Vmn1r128	A	G	7: 21,083,740 (GRCm39)	Y148C	possibly damaging	Het
Vmn1r193	T	C	13: 22,403,839 (GRCm39)	Y51C	probably benign	Het
Vmn2r112	A	G	17: 22,837,612 (GRCm39)	Y691C	probably damaging	Het
Vmn2r25	T	A	6: 123,800,569 (GRCm39)	D591V	probably damaging	Het
Vmn2r94	A	G	17: 18,464,335 (GRCm39)	S652P	possibly damaging	Het
Vps50	T	A	6: 3,536,967 (GRCm39)	C313S	probably damaging	Het
Vwa5b1	A	G	4: 138,338,041 (GRCm39)	V93A	probably benign	Het
Xrcc5	T	G	1: 72,382,190 (GRCm39)	D455E	possibly damaging	Het
Zdhhc6	T	A	19: 55,290,987 (GRCm39)		probably benign	Het
Zfp964	G	A	8: 70,116,405 (GRCm39)	G335D	probably damaging	Het

Other mutations in Sox2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02578:Sox2	APN	3	34,704,745 (GRCm39)	missense	probably benign	0.37
IGL03397:Sox2	APN	3	34,704,686 (GRCm39)	missense	probably damaging	0.99
R1164:Sox2	UTSW	3	34,704,848 (GRCm39)	missense	probably damaging	1.00
R1667:Sox2	UTSW	3	34,704,568 (GRCm39)	missense	probably damaging	1.00
R1829:Sox2	UTSW	3	34,704,890 (GRCm39)	missense	probably damaging	0.99
R1925:Sox2	UTSW	3	34,704,820 (GRCm39)	nonsense	probably null
R2066:Sox2	UTSW	3	34,705,456 (GRCm39)	missense	possibly damaging	0.63
R4170:Sox2	UTSW	3	34,704,703 (GRCm39)	missense	probably damaging	0.99
R4585:Sox2	UTSW	3	34,705,193 (GRCm39)	missense	probably benign	0.02
R4586:Sox2	UTSW	3	34,705,193 (GRCm39)	missense	probably benign	0.02
R4703:Sox2	UTSW	3	34,704,862 (GRCm39)	missense	probably damaging	1.00
R5509:Sox2	UTSW	3	34,704,938 (GRCm39)	missense	probably damaging	0.98
R5549:Sox2	UTSW	3	34,705,142 (GRCm39)	missense	probably benign	0.01
R5637:Sox2	UTSW	3	34,704,677 (GRCm39)	missense	probably benign	0.03
R6494:Sox2	UTSW	3	34,705,246 (GRCm39)	missense	probably benign	0.01
R7117:Sox2	UTSW	3	34,705,075 (GRCm39)	missense	possibly damaging	0.95
R7210:Sox2	UTSW	3	34,705,306 (GRCm39)	missense	probably damaging	1.00
R7365:Sox2	UTSW	3	34,705,121 (GRCm39)	missense	possibly damaging	0.60
R7798:Sox2	UTSW	3	34,704,791 (GRCm39)	missense	probably damaging	0.96
R7801:Sox2	UTSW	3	34,704,791 (GRCm39)	missense	probably damaging	0.96
R8684:Sox2	UTSW	3	34,705,016 (GRCm39)	missense	probably benign	0.00
R9013:Sox2	UTSW	3	34,704,746 (GRCm39)	missense	probably damaging	1.00
X0024:Sox2	UTSW	3	34,704,838 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CCGGATTATAAATACCGGCCGC -3'
(R):5'- ACTTGACCACAGAGCCCATG -3'

Sequencing Primer
(F):5'- GATAAGTACACGCTTCCCGGAG -3'
(R):5'- ACAGAGCCCATGGAGCC -3'

Posted On

2021-08-02