Mutagenetix > Incidental Mutation

Incidental Mutation 'R6249:Sox5'

505844

Institutional Source

Beutler Lab

Gene Symbol

Sox5

Ensembl Gene

ENSMUSG00000041540

Gene Name

SRY (sex determining region Y)-box 5

Synonyms

A730017D01Rik

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6249 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

143774151-144727703 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 143779009 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 674 (I674T)

Ref Sequence

ENSEMBL: ENSMUSP00000107378 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000038815
AA Change: I758T

PolyPhen 2 Score 0.097 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000047567
Gene: ENSMUSG00000041540
AA Change: I758T

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: I710T

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000076403
Gene: ENSMUSG00000041540
AA Change: I710T

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

probably benign
Transcript: ENSMUST00000111748
AA Change: I387T

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000107377
Gene: ENSMUSG00000041540
AA Change: I387T

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: I674T

PolyPhen 2 Score 0.332 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000107378
Gene: ENSMUSG00000041540
AA Change: I674T

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

probably benign
Transcript: ENSMUST00000170367
AA Change: I709T

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000133041
Gene: ENSMUSG00000041540
AA Change: I709T

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: 99.9%
3x: 99.7%
10x: 98.5%
20x: 95.8%

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110004F10Rik	A	T	7: 115,702,505 (GRCm39)	S90C	probably damaging	Het
Abca9	T	C	11: 110,036,453 (GRCm39)	D552G	probably benign	Het
Adgrb3	A	G	1: 25,471,639 (GRCm39)	L502P	probably damaging	Het
Agmo	T	C	12: 37,293,837 (GRCm39)		probably null	Het
Ank3	A	G	10: 69,658,906 (GRCm39)		probably null	Het
Apol11b	G	T	15: 77,519,537 (GRCm39)	T181K	probably benign	Het
Arap2	G	T	5: 62,803,536 (GRCm39)	H1244N	probably damaging	Het
Arid1b	A	T	17: 5,329,636 (GRCm39)	M838L	possibly damaging	Het
Aste1	G	A	9: 105,273,816 (GRCm39)	V19I	probably benign	Het
B3gnt3	A	T	8: 72,145,306 (GRCm39)	M354K	probably damaging	Het
Calcr	A	T	6: 3,692,711 (GRCm39)	M381K	possibly damaging	Het
Ccdc63	A	C	5: 122,263,062 (GRCm39)	L160W	probably benign	Het
Cerkl	A	G	2: 79,199,122 (GRCm39)	L156P	probably damaging	Het
Csnk2a1-ps3	A	G	1: 156,352,800 (GRCm39)	M334V	probably benign	Het
Dab1	C	T	4: 104,588,948 (GRCm39)	A524V	probably benign	Het
Ddb1	C	A	19: 10,583,084 (GRCm39)	Y5*	probably null	Het
Fignl2	T	C	15: 100,952,060 (GRCm39)	E74G	possibly damaging	Het
Glb1l2	C	T	9: 26,676,850 (GRCm39)		probably benign	Het
Gm16503	A	G	4: 147,625,508 (GRCm39)	M1V	probably null	Het
Gm2696	A	C	10: 77,630,646 (GRCm39)		probably benign	Het
Gm45844	A	G	7: 7,243,092 (GRCm39)	S20P	probably benign	Het
Gm7579	C	T	7: 141,765,743 (GRCm39)	P50S	unknown	Het
Idh1	A	G	1: 65,205,378 (GRCm39)	S196P	probably damaging	Het
Il1rap	T	C	16: 26,511,598 (GRCm39)	V214A	possibly damaging	Het
Kctd17	C	G	15: 78,314,239 (GRCm39)		probably null	Het
Lama1	G	T	17: 68,105,599 (GRCm39)	V2036L	probably benign	Het
Lars1	G	T	18: 42,390,271 (GRCm39)		probably null	Het
Mdn1	T	A	4: 32,708,484 (GRCm39)	V1670E	possibly damaging	Het
Mtmr7	A	T	8: 41,034,524 (GRCm39)	I266N	probably damaging	Het
Ncapd3	GGCTGCTGCTGCTGCTGCTGCTG	GGCTGCTGCTGCTGCTGCTG	9: 26,999,349 (GRCm39)		probably benign	Het
Nckap5	T	C	1: 125,952,667 (GRCm39)	E1295G	probably benign	Het
Nrxn3	T	A	12: 89,221,448 (GRCm39)	V409D	probably damaging	Het
Or13p3	A	G	4: 118,566,910 (GRCm39)	Y102C	probably damaging	Het
Or2a5	G	T	6: 42,874,238 (GRCm39)	L284F	probably damaging	Het
Or2aj4	T	A	16: 19,384,725 (GRCm39)	N303Y	probably damaging	Het
Or51q1	A	T	7: 103,628,818 (GRCm39)	S140C	possibly damaging	Het
Or5h22	T	C	16: 58,894,795 (GRCm39)	Y216C	probably damaging	Het
Or8b44	T	G	9: 38,410,880 (GRCm39)	I305R	unknown	Het
Pcdha4	T	A	18: 37,086,729 (GRCm39)	V304E	probably damaging	Het
Pde6c	T	C	19: 38,147,008 (GRCm39)		probably null	Het
Pebp4	A	T	14: 70,297,099 (GRCm39)	T213S	possibly damaging	Het
Phf2	C	A	13: 48,959,348 (GRCm39)	R886L	unknown	Het
Pik3ca	A	T	3: 32,515,712 (GRCm39)	H795L	probably damaging	Het
Pisd	G	T	5: 32,896,188 (GRCm39)	T379N	probably damaging	Het
Pld2	T	C	11: 70,446,196 (GRCm39)	L732P	probably damaging	Het
Pskh1	A	G	8: 106,639,617 (GRCm39)	D99G	possibly damaging	Het
Rest	A	G	5: 77,429,071 (GRCm39)	T497A	probably benign	Het
Rps24	C	T	14: 24,543,530 (GRCm39)	T108M	possibly damaging	Het
Rtel1	C	T	2: 180,993,475 (GRCm39)	R566C	probably damaging	Het
Scyl2	A	G	10: 89,493,719 (GRCm39)	S350P	possibly damaging	Het
Slc38a7	G	T	8: 96,564,302 (GRCm39)		probably null	Het
Spata31f1a	A	T	4: 42,850,528 (GRCm39)	W543R	probably benign	Het
Surf4	C	A	2: 26,816,899 (GRCm39)	E39D	probably damaging	Het
Tas2r144	T	A	6: 42,192,291 (GRCm39)	Y10*	probably null	Het
Thbs4	C	T	13: 92,911,215 (GRCm39)	G323R	probably damaging	Het
Top2b	A	G	14: 16,399,006 (GRCm38)	Y542C	probably damaging	Het
Trim61	A	G	8: 65,467,108 (GRCm39)	V51A	probably benign	Het
Tyrp1	T	A	4: 80,769,009 (GRCm39)	I501N	possibly damaging	Het
U2surp	C	T	9: 95,382,869 (GRCm39)	D32N	probably benign	Het
Ush1c	T	C	7: 45,864,383 (GRCm39)	Y411C	probably damaging	Het
Vwa7	G	A	17: 35,242,365 (GRCm39)	V490I	probably benign	Het
Xylt1	G	T	7: 117,266,528 (GRCm39)	A849S	probably benign	Het
Ythdc1	T	A	5: 86,979,815 (GRCm39)	N599K	possibly damaging	Het
Zbtb38	T	A	9: 96,568,045 (GRCm39)	Y1013F	probably damaging	Het
Zfp709	TCGACG	TCG	8: 72,644,552 (GRCm39)		probably benign	Het
Zswim9	T	C	7: 12,994,903 (GRCm39)	S418G	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
R1959:Sox5	UTSW	6	143,819,831 (GRCm39)	missense	possibly damaging	0.94
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
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'- GGTCTATTTGTCAGCTGATGTCCC -3'
(R):5'- TTTCTGTGACAGGCAACAAGC -3'

Sequencing Primer
(F):5'- GTCAGCTGATGTCCCAACTATATAAG -3'
(R):5'- AGTTGTATACCCCAGCGCC -3'

Posted On

2018-02-28