Mutagenetix > Incidental Mutation

Incidental Mutation 'R1959:Sox5'

218146

Institutional Source

Beutler Lab

Gene Symbol

Sox5

Ensembl Gene

ENSMUSG00000041540

Gene Name

SRY (sex determining region Y)-box 5

Synonyms

A730017D01Rik

MMRRC Submission

039973-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1959 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

143774151-144727703 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 143819831 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 62 (S62P)

Ref Sequence

ENSEMBL: ENSMUSP00000114602 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038815] [ENSMUST00000077160] [ENSMUST00000111748] [ENSMUST00000111749] [ENSMUST00000124233] [ENSMUST00000144289] [ENSMUST00000170367]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000038815
AA Change: S404P

PolyPhen 2 Score 0.676 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000047567
Gene: ENSMUSG00000041540
AA Change: S404P

Domain	Start	End	E-Value	Type
low complexity region	167	178	N/A	INTRINSIC
coiled coil region	193	272	N/A	INTRINSIC
low complexity region	336	348	N/A	INTRINSIC
low complexity region	431	445	N/A	INTRINSIC
coiled coil region	449	483	N/A	INTRINSIC
low complexity region	494	505	N/A	INTRINSIC
HMG	555	625	2.84e-26	SMART
low complexity region	686	708	N/A	INTRINSIC
low complexity region	729	750	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000077160
AA Change: S356P

PolyPhen 2 Score 0.209 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000076403
Gene: ENSMUSG00000041540
AA Change: S356P

Domain	Start	End	E-Value	Type
low complexity region	167	178	N/A	INTRINSIC
coiled coil region	193	277	N/A	INTRINSIC
low complexity region	383	397	N/A	INTRINSIC
coiled coil region	401	435	N/A	INTRINSIC
low complexity region	446	457	N/A	INTRINSIC
HMG	507	577	2.84e-26	SMART
low complexity region	638	660	N/A	INTRINSIC
low complexity region	681	702	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000111746

SMART Domains

Protein: ENSMUSP00000107375
Gene: ENSMUSG00000041540

Domain	Start	End	E-Value	Type
low complexity region	60	74	N/A	INTRINSIC
coiled coil region	78	112	N/A	INTRINSIC
low complexity region	123	134	N/A	INTRINSIC
HMG	184	234	1.72e-2	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000111748
AA Change: S33P

PolyPhen 2 Score 0.209 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000107377
Gene: ENSMUSG00000041540
AA Change: S33P

Domain	Start	End	E-Value	Type
low complexity region	60	74	N/A	INTRINSIC
coiled coil region	78	112	N/A	INTRINSIC
low complexity region	123	134	N/A	INTRINSIC
HMG	184	254	2.84e-26	SMART
low complexity region	315	337	N/A	INTRINSIC
low complexity region	358	379	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000111749
AA Change: S320P

PolyPhen 2 Score 0.073 (Sensitivity: 0.93; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000107378
Gene: ENSMUSG00000041540
AA Change: S320P

Domain	Start	End	E-Value	Type
low complexity region	132	143	N/A	INTRINSIC
coiled coil region	158	237	N/A	INTRINSIC
low complexity region	347	361	N/A	INTRINSIC
coiled coil region	365	399	N/A	INTRINSIC
low complexity region	410	421	N/A	INTRINSIC
HMG	471	541	2.84e-26	SMART
low complexity region	602	624	N/A	INTRINSIC
low complexity region	645	666	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000124233
AA Change: S62P

PolyPhen 2 Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000114602
Gene: ENSMUSG00000041540
AA Change: S62P

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
low complexity region	89	103	N/A	INTRINSIC
coiled coil region	107	141	N/A	INTRINSIC
low complexity region	152	163	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141102

Predicted Effect

possibly damaging
Transcript: ENSMUST00000144289
AA Change: S82P

PolyPhen 2 Score 0.827 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000122786
Gene: ENSMUSG00000041540
AA Change: S82P

Domain	Start	End	E-Value	Type
low complexity region	14	26	N/A	INTRINSIC
low complexity region	109	123	N/A	INTRINSIC
coiled coil region	127	161	N/A	INTRINSIC
low complexity region	172	183	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000170367
AA Change: S355P

PolyPhen 2 Score 0.209 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000133041
Gene: ENSMUSG00000041540
AA Change: S355P

Domain	Start	End	E-Value	Type
low complexity region	167	178	N/A	INTRINSIC
coiled coil region	193	272	N/A	INTRINSIC
low complexity region	382	396	N/A	INTRINSIC
coiled coil region	400	434	N/A	INTRINSIC
low complexity region	445	456	N/A	INTRINSIC
HMG	506	576	2.84e-26	SMART
low complexity region	637	659	N/A	INTRINSIC
low complexity region	680	701	N/A	INTRINSIC

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.5%
20x: 93.2%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. The encoded protein may play a role in chondrogenesis. A pseudogene of this gene is located on chromosome 8. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous null mice fail to breathe and die at birth exhibiting a narrow thoracic cage, irregularly mineralized sternum, cleft secondary palate, and delayed bone mineralization. Homozygotes for a transposon induced insertion die shortly after birth exhibiting cyanosis and respiratory distress. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 130 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc1	T	C	16: 14,214,257 (GRCm39)	Y191H	probably damaging	Het
Aco1	T	C	4: 40,167,193 (GRCm39)		probably null	Het
Adap1	A	G	5: 139,259,096 (GRCm39)	Y364H	probably benign	Het
Add2	T	C	6: 86,073,738 (GRCm39)	F209S	probably damaging	Het
Adgb	A	T	10: 10,270,993 (GRCm39)	D883E	probably benign	Het
Anapc1	C	A	2: 128,475,335 (GRCm39)	R1381S	probably benign	Het
Aoah	A	G	13: 20,978,564 (GRCm39)	M1V	probably null	Het
Arap1	C	A	7: 101,022,222 (GRCm39)	A8E	probably damaging	Het
Arhgap10	A	G	8: 78,136,255 (GRCm39)	F319S	possibly damaging	Het
Btrc	T	G	19: 45,515,782 (GRCm39)	I480S	probably damaging	Het
Cabin1	A	T	10: 75,570,924 (GRCm39)	V784E	possibly damaging	Het
Card9	T	A	2: 26,244,885 (GRCm39)		probably null	Het
Cdk18	A	G	1: 132,045,559 (GRCm39)	I238T	possibly damaging	Het
Clec12a	A	C	6: 129,327,444 (GRCm39)	T21P	possibly damaging	Het
Commd3	A	T	2: 18,678,774 (GRCm39)	I70F	probably benign	Het
Cspg5	G	A	9: 110,080,094 (GRCm39)	V340M	probably damaging	Het
Cyb5r4	G	A	9: 86,937,902 (GRCm39)	S307N	possibly damaging	Het
Cyp26c1	T	A	19: 37,675,825 (GRCm39)	F230I	probably damaging	Het
Ddx11	A	G	17: 66,437,723 (GRCm39)	M150V	probably benign	Het
Dennd4b	A	G	3: 90,176,080 (GRCm39)	Y190C	probably damaging	Het
Det1	A	G	7: 78,493,191 (GRCm39)	V271A	probably benign	Het
Dgkd	C	A	1: 87,857,549 (GRCm39)	P754T	possibly damaging	Het
Dhx36	T	C	3: 62,386,806 (GRCm39)	S649G	probably benign	Het
Dlgap5	A	G	14: 47,653,843 (GRCm39)	I62T	possibly damaging	Het
Dmgdh	A	G	13: 93,857,067 (GRCm39)	M724V	probably benign	Het
Dnah7a	A	G	1: 53,724,142 (GRCm39)	S108P	probably benign	Het
Dock4	A	T	12: 40,760,797 (GRCm39)	K495M	probably damaging	Het
Dse	A	G	10: 34,036,202 (GRCm39)	Y225H	probably damaging	Het
Emx1	G	A	6: 85,180,916 (GRCm39)	R211K	probably damaging	Het
Ergic2	A	G	6: 148,100,852 (GRCm39)		probably null	Het
Fbxo27	G	A	7: 28,397,797 (GRCm39)	C277Y	possibly damaging	Het
Fcrl1	T	C	3: 87,283,827 (GRCm39)	I9T	possibly damaging	Het
Fjx1	T	C	2: 102,281,152 (GRCm39)	E261G	probably benign	Het
Flacc1	A	T	1: 58,698,437 (GRCm39)	V327D	possibly damaging	Het
Flnb	C	T	14: 7,884,735 (GRCm38)	Q445*	probably null	Het
Flrt2	G	A	12: 95,747,074 (GRCm39)	V471I	probably benign	Het
Frmd4a	G	A	2: 4,539,997 (GRCm39)	V210M	probably damaging	Het
Fsip2	A	G	2: 82,821,894 (GRCm39)	K5876E	probably benign	Het
Galnt10	T	C	11: 57,656,443 (GRCm39)	L209P	probably damaging	Het
Gata5	A	T	2: 179,968,729 (GRCm39)	S382T	possibly damaging	Het
Glt6d1	C	A	2: 25,684,425 (GRCm39)	V194L	probably damaging	Het
Gm10803	T	G	2: 93,394,288 (GRCm39)	V20G	unknown	Het
Gm44511	T	G	6: 128,797,234 (GRCm39)	T52P	probably damaging	Het
Gpat4	A	T	8: 23,672,952 (GRCm39)	L88Q	possibly damaging	Het
Gpr15	T	A	16: 58,538,370 (GRCm39)	I240L	probably benign	Het
Hivep2	A	T	10: 14,008,453 (GRCm39)	I1684F	probably benign	Het
Hmcn1	T	C	1: 150,525,427 (GRCm39)	T3366A	probably benign	Het
Hnmt	A	G	2: 23,893,894 (GRCm39)	V200A	possibly damaging	Het
Hps6	A	T	19: 45,992,774 (GRCm39)	H237L	probably benign	Het
Hspg2	C	T	4: 137,292,206 (GRCm39)	P4033S	probably damaging	Het
Ift70b	C	T	2: 75,767,443 (GRCm39)	E437K	probably benign	Het
Irf9	T	A	14: 55,845,174 (GRCm39)	S297T	possibly damaging	Het
Kdm3b	T	C	18: 34,945,448 (GRCm39)	V753A	possibly damaging	Het
Kif21a	G	A	15: 90,855,051 (GRCm39)	A703V	probably damaging	Het
Kif27	T	G	13: 58,440,937 (GRCm39)	R1159S	probably benign	Het
Krtap4-16	A	G	11: 99,742,373 (GRCm39)	V9A	unknown	Het
Lama2	G	T	10: 27,298,614 (GRCm39)	P161T	probably damaging	Het
Ltbp4	G	A	7: 27,028,443 (GRCm39)	P273L	unknown	Het
Lvrn	T	A	18: 47,027,784 (GRCm39)	S866R	probably damaging	Het
Med13	A	G	11: 86,189,805 (GRCm39)	Y1035H	probably damaging	Het
Mertk	T	A	2: 128,601,010 (GRCm39)	N331K	probably damaging	Het
Mios	T	A	6: 8,215,437 (GRCm39)	F211Y	probably benign	Het
Mpeg1	G	A	19: 12,440,275 (GRCm39)	V578M	probably damaging	Het
Mphosph9	A	T	5: 124,453,764 (GRCm39)	S183T	possibly damaging	Het
Mrto4	A	T	4: 139,076,949 (GRCm39)	I56N	probably damaging	Het
Muc5b	T	C	7: 141,416,374 (GRCm39)	C3107R	possibly damaging	Het
Ncoa2	A	G	1: 13,230,476 (GRCm39)	Y1023H	probably damaging	Het
Nlrp2	T	C	7: 5,330,737 (GRCm39)	E553G	probably damaging	Het
Nlrp6	GAGAAGAAGAAGAAGAAGAAGA	GAGAAGAAGAAGAAGAAGA	7: 140,504,026 (GRCm39)		probably benign	Het
Nr2f1	T	C	13: 78,337,935 (GRCm39)	T237A	probably damaging	Het
Nup205	C	A	6: 35,210,301 (GRCm39)	Q1621K	probably benign	Het
Nup50l	A	G	6: 96,142,250 (GRCm39)	S265P	possibly damaging	Het
Nxpe2	T	A	9: 48,231,026 (GRCm39)	S448C	probably benign	Het
Ogdh	T	A	11: 6,296,638 (GRCm39)	C498S	possibly damaging	Het
Oplah	G	A	15: 76,181,664 (GRCm39)	T1119I	probably damaging	Het
Or14a256	A	T	7: 86,265,639 (GRCm39)	F71L	probably benign	Het
Or2ag15	T	C	7: 106,340,601 (GRCm39)	E180G	probably damaging	Het
Or2d2	A	T	7: 106,727,717 (GRCm39)	D294E	possibly damaging	Het
Or5ak24	T	C	2: 85,260,963 (GRCm39)	D70G	probably damaging	Het
Or5d46	T	C	2: 88,170,545 (GRCm39)	L212P	probably damaging	Het
Or6p1	A	T	1: 174,258,471 (GRCm39)	K159M	probably damaging	Het
Or8s8	T	C	15: 98,354,634 (GRCm39)	S148P	probably damaging	Het
Pcdhb9	T	A	18: 37,536,369 (GRCm39)	Y788N	probably damaging	Het
Pcsk5	T	C	19: 17,410,782 (GRCm39)	D1870G	unknown	Het
Pde6g	A	G	11: 120,338,962 (GRCm39)	L76P	probably damaging	Het
Peak1	A	T	9: 56,114,073 (GRCm39)	Y593N	probably damaging	Het
Pfas	C	T	11: 68,885,110 (GRCm39)	G16R	probably damaging	Het
Pkd1l2	A	T	8: 117,769,970 (GRCm39)		probably null	Het
Pla2g3	C	T	11: 3,440,983 (GRCm39)	T316I	probably benign	Het
Ptpru	T	A	4: 131,530,788 (GRCm39)	I489F	probably damaging	Het
Rere	T	G	4: 150,553,247 (GRCm39)	H146Q	probably benign	Het
Rundc1	A	T	11: 101,322,322 (GRCm39)	Q272L	probably damaging	Het
Scml4	T	C	10: 42,832,017 (GRCm39)	L305P	probably damaging	Het
Sec16a	A	T	2: 26,320,144 (GRCm39)	H1431Q	probably benign	Het
Serpina1a	G	A	12: 103,820,059 (GRCm39)	Q373*	probably null	Het
Shank1	A	T	7: 43,974,801 (GRCm39)	N377I	unknown	Het
Shc2	T	C	10: 79,462,625 (GRCm39)		probably null	Het
Slc22a29	C	A	19: 8,146,557 (GRCm39)	R415M	probably benign	Het
Slc7a2	A	T	8: 41,368,002 (GRCm39)	I589F	probably damaging	Het
Smim8	C	T	4: 34,771,316 (GRCm39)	R26Q	probably damaging	Het
Smox	C	A	2: 131,362,384 (GRCm39)	A221D	probably damaging	Het
Spg21	A	C	9: 65,391,774 (GRCm39)	K240N	probably damaging	Het
Sv2c	C	T	13: 96,113,153 (GRCm39)	V599M	probably damaging	Het
Tanc2	T	A	11: 105,801,121 (GRCm39)	H1112Q	probably damaging	Het
Tbata	T	C	10: 61,011,623 (GRCm39)	I58T	possibly damaging	Het
Tbc1d2	T	G	4: 46,606,419 (GRCm39)	Y842S	probably benign	Het
Tctn1	A	T	5: 122,379,903 (GRCm39)		probably null	Het
Tenm1	T	C	X: 41,916,078 (GRCm39)	D402G	probably benign	Het
Tfcp2l1	T	C	1: 118,597,119 (GRCm39)	V400A	probably benign	Het
Tm9sf2	T	A	14: 122,363,576 (GRCm39)	L99I	probably benign	Het
Top2a	T	C	11: 98,886,803 (GRCm39)		probably null	Het
Traf7	C	A	17: 24,732,255 (GRCm39)	G191C	probably damaging	Het
Trpm1	T	A	7: 63,879,978 (GRCm39)	L661Q	probably damaging	Het
Ttn	T	C	2: 76,580,967 (GRCm39)	I23309V	probably benign	Het
Usp50	T	C	2: 126,619,881 (GRCm39)	K199E	possibly damaging	Het
Vmn1r218	T	C	13: 23,320,683 (GRCm39)	F10S	probably damaging	Het
Vmn2r89	C	A	14: 51,694,897 (GRCm39)	T459K	probably benign	Het
Vps13a	T	G	19: 16,655,302 (GRCm39)	S1909R	possibly damaging	Het
Vwa5b2	T	C	16: 20,420,941 (GRCm39)		probably null	Het
Vwa8	A	G	14: 79,219,800 (GRCm39)	H516R	possibly damaging	Het
Wnk1	T	C	6: 119,946,208 (GRCm39)	I648M	probably damaging	Het
Zfat	G	C	15: 68,018,392 (GRCm39)	P974R	probably benign	Het
Zfc3h1	T	A	10: 115,259,158 (GRCm39)	I1601K	probably benign	Het
Zfp239	A	G	6: 117,848,778 (GRCm39)	K172R	probably benign	Het
Zfp335	C	T	2: 164,736,722 (GRCm39)	G971D	probably damaging	Het
Zfp532	A	T	18: 65,757,563 (GRCm39)	I499F	probably damaging	Het
Zfp647	T	C	15: 76,795,314 (GRCm39)	T449A	possibly damaging	Het
Zfp938	C	T	10: 82,061,465 (GRCm39)	G385D	probably damaging	Het
Zfp959	T	G	17: 56,204,404 (GRCm39)	V147G	probably damaging	Het
Znfx1	A	T	2: 166,892,270 (GRCm39)	C649S	probably damaging	Het

Other mutations in Sox5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01364:Sox5	APN	6	144,062,198 (GRCm39)	missense	probably damaging	0.96
IGL03217:Sox5	APN	6	143,853,223 (GRCm39)	missense	probably damaging	1.00
Stocking	UTSW	6	144,062,169 (GRCm39)	critical splice donor site	probably null
R0230:Sox5	UTSW	6	144,155,064 (GRCm39)	missense	probably benign	0.02
R0610:Sox5	UTSW	6	143,779,165 (GRCm39)	missense	possibly damaging	0.56
R1162:Sox5	UTSW	6	143,906,538 (GRCm39)	missense	probably damaging	1.00
R1857:Sox5	UTSW	6	143,906,541 (GRCm39)	missense	probably damaging	1.00
R4057:Sox5	UTSW	6	144,062,248 (GRCm39)	missense	probably damaging	1.00
R4164:Sox5	UTSW	6	144,062,206 (GRCm39)	missense	probably damaging	1.00
R4284:Sox5	UTSW	6	143,781,055 (GRCm39)	missense	probably damaging	1.00
R4430:Sox5	UTSW	6	143,987,000 (GRCm39)	missense	possibly damaging	0.57
R4470:Sox5	UTSW	6	143,790,491 (GRCm39)	missense	possibly damaging	0.54
R4471:Sox5	UTSW	6	143,790,491 (GRCm39)	missense	possibly damaging	0.54
R4672:Sox5	UTSW	6	143,779,075 (GRCm39)	missense	probably damaging	1.00
R4683:Sox5	UTSW	6	143,779,193 (GRCm39)	missense	probably damaging	0.99
R4693:Sox5	UTSW	6	143,781,042 (GRCm39)	missense	probably damaging	1.00
R4735:Sox5	UTSW	6	143,906,561 (GRCm39)	missense	probably damaging	1.00
R4745:Sox5	UTSW	6	143,779,214 (GRCm39)	missense	possibly damaging	0.53
R4762:Sox5	UTSW	6	143,807,109 (GRCm39)	critical splice donor site	probably null
R4996:Sox5	UTSW	6	143,974,070 (GRCm39)	nonsense	probably null
R5218:Sox5	UTSW	6	143,906,616 (GRCm39)	missense	possibly damaging	0.93
R5673:Sox5	UTSW	6	144,062,206 (GRCm39)	missense	probably damaging	1.00
R5856:Sox5	UTSW	6	144,155,088 (GRCm39)	missense	probably damaging	1.00
R6249:Sox5	UTSW	6	143,779,009 (GRCm39)	missense	probably benign	0.33
R6394:Sox5	UTSW	6	143,987,039 (GRCm39)	missense	probably damaging	1.00
R6703:Sox5	UTSW	6	143,779,191 (GRCm39)	missense	probably damaging	1.00
R6812:Sox5	UTSW	6	144,062,169 (GRCm39)	critical splice donor site	probably null
R7312:Sox5	UTSW	6	144,100,759 (GRCm39)	missense	probably benign
R7543:Sox5	UTSW	6	143,786,905 (GRCm39)	missense	probably damaging	0.96
R8110:Sox5	UTSW	6	144,062,200 (GRCm39)	missense	possibly damaging	0.92
R8231:Sox5	UTSW	6	143,974,014 (GRCm39)	missense	probably damaging	0.98
R8250:Sox5	UTSW	6	144,100,777 (GRCm39)	missense	possibly damaging	0.85
R8705:Sox5	UTSW	6	143,987,012 (GRCm39)	missense	possibly damaging	0.50
R8937:Sox5	UTSW	6	143,853,169 (GRCm39)	missense	probably benign	0.00
R9182:Sox5	UTSW	6	143,779,118 (GRCm39)	missense	possibly damaging	0.51
R9193:Sox5	UTSW	6	143,790,570 (GRCm39)	missense	probably benign	0.27
R9740:Sox5	UTSW	6	144,100,947 (GRCm39)	missense	probably damaging	0.98
R9762:Sox5	UTSW	6	143,819,842 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGCCGTGAATGGGAAATCAATG -3'
(R):5'- TGTGAGCTTCCTGTTGCAC -3'

Sequencing Primer
(F):5'- CCGTGAATGGGAAATCAATGAGAAC -3'
(R):5'- GAGCTTCCTGTTGCACAACCAG -3'

Posted On

2014-08-01