Mutagenetix > Incidental Mutation

Incidental Mutation 'R2029:Skint1'

220919

Institutional Source

Beutler Lab

Gene Symbol

Skint1

Ensembl Gene

ENSMUSG00000089773

Gene Name

selection and upkeep of intraepithelial T cells 1

Synonyms

MMRRC Submission

040036-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.063) question?

Stock #

R2029 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

111863466-111886735 bp(+) (GRCm39)

Type of Mutation

splice site (2050 bp from exon)

DNA Base Change (assembly)

G to A at 111878653 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000125625 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000117379] [ENSMUST00000161389] [ENSMUST00000162158] [ENSMUST00000162885]

AlphaFold

A7TZE6

Predicted Effect

probably benign
Transcript: ENSMUST00000117379
AA Change: R195K

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000124545
Gene: ENSMUSG00000089773
AA Change: R195K

Domain	Start	End	E-Value	Type
IGv	44	125	1.88e-8	SMART
Pfam:C2-set_2	142	228	2.5e-6	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000161389
AA Change: R195K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000125313
Gene: ENSMUSG00000089773
AA Change: R195K

Domain	Start	End	E-Value	Type
IGv	44	125	1.88e-8	SMART
Pfam:C2-set_2	142	228	3.1e-6	PFAM
transmembrane domain	248	267	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000162158
AA Change: R195K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000124737
Gene: ENSMUSG00000089773
AA Change: R195K

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
IGv	44	125	1.88e-8	SMART
transmembrane domain	247	269	N/A	INTRINSIC
transmembrane domain	282	304	N/A	INTRINSIC
transmembrane domain	326	348	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000162885

SMART Domains

Protein: ENSMUSP00000125625
Gene: ENSMUSG00000089773

Domain	Start	End	E-Value	Type
IGv	44	125	1.88e-8	SMART

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 93.8%

Validation Efficiency

98% (97/99)

MGI Phenotype

PHENOTYPE: Mice homozygous for a point mutation allele exhibit impaired T cell differentiation with reduced Vgamma5+Vdelta1+ T cells. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam18	C	G	8: 25,140,893 (GRCm39)	G286A	probably damaging	Het
Adcy1	G	A	11: 7,089,142 (GRCm39)	A519T	probably benign	Het
Anxa2	T	A	9: 69,371,762 (GRCm39)	S2T	possibly damaging	Het
Ap3m1	G	A	14: 21,089,217 (GRCm39)	S261L	possibly damaging	Het
Baz2b	A	T	2: 59,743,067 (GRCm39)		probably benign	Het
Brdt	T	A	5: 107,507,090 (GRCm39)	S497T	probably benign	Het
Cdh11	A	G	8: 103,406,404 (GRCm39)	F23S	probably benign	Het
Cdh16	A	C	8: 105,344,434 (GRCm39)	L540R	probably damaging	Het
Ces5a	A	T	8: 94,261,205 (GRCm39)	L74Q	probably damaging	Het
Cfap69	A	G	5: 5,654,306 (GRCm39)	S543P	probably damaging	Het
Cfap74	T	C	4: 155,526,538 (GRCm39)	I763T	possibly damaging	Het
Cma1	T	A	14: 56,181,191 (GRCm39)	R58S	possibly damaging	Het
Csmd3	C	T	15: 47,701,975 (GRCm39)	D1599N	probably damaging	Het
Cyld	A	G	8: 89,471,940 (GRCm39)	K857R	probably benign	Het
Cyp3a16	T	C	5: 145,388,667 (GRCm39)	D270G	probably damaging	Het
D1Pas1	T	C	1: 186,700,286 (GRCm39)	S72P	possibly damaging	Het
Ddx3y	T	C	Y: 1,266,389 (GRCm39)	E331G	probably benign	Het
Degs1l	T	A	1: 180,882,496 (GRCm39)	I86K	probably benign	Het
Dis3l2	T	C	1: 86,782,189 (GRCm39)		probably benign	Het
Dop1a	G	T	9: 86,403,418 (GRCm39)	W1539C	probably damaging	Het
Dop1b	A	G	16: 93,566,323 (GRCm39)	K917E	probably benign	Het
Ecpas	G	A	4: 58,844,165 (GRCm39)	R534*	probably null	Het
Efcab3	T	C	11: 104,990,851 (GRCm39)	I5462T	probably damaging	Het
Eif1ad15	A	T	12: 88,288,191 (GRCm39)	S21T	unknown	Het
Epo	A	G	5: 137,483,447 (GRCm39)		probably benign	Het
Figla	T	A	6: 85,997,624 (GRCm39)		probably benign	Het
Flvcr1	T	C	1: 190,753,353 (GRCm39)	D273G	probably benign	Het
Fryl	T	A	5: 73,179,465 (GRCm39)	R304*	probably null	Het
Gcm1	T	G	9: 77,972,326 (GRCm39)	D422E	possibly damaging	Het
Get3	A	T	8: 85,746,403 (GRCm39)	Y148*	probably null	Het
Ggt6	A	G	11: 72,328,367 (GRCm39)	D251G	possibly damaging	Het
Git2	A	G	5: 114,904,511 (GRCm39)		probably null	Het
Gm18856	A	T	13: 14,139,376 (GRCm39)		probably benign	Het
Gm20939	T	A	17: 95,183,252 (GRCm39)		probably benign	Het
Gpr176	A	G	2: 118,109,913 (GRCm39)	Y449H	probably benign	Het
H2-Eb1	A	G	17: 34,533,366 (GRCm39)	E196G	probably damaging	Het
H2-M10.6	A	G	17: 37,124,799 (GRCm39)	T239A	possibly damaging	Het
Haus5	T	C	7: 30,358,825 (GRCm39)	N237S	possibly damaging	Het
Hectd3	T	C	4: 116,857,882 (GRCm39)	M605T	probably damaging	Het
Hps3	T	C	3: 20,084,691 (GRCm39)	I166V	probably benign	Het
Ighv5-21	A	T	12: 114,286,434 (GRCm39)		probably benign	Het
Kdm6b	C	T	11: 69,294,418 (GRCm39)	G1218D	unknown	Het
Klhl30	A	G	1: 91,285,636 (GRCm39)		probably null	Het
Kmt2a	A	T	9: 44,729,747 (GRCm39)	S3523R	probably benign	Het
Lnpep	A	T	17: 17,788,661 (GRCm39)	N481K	probably damaging	Het
Lrp1b	T	C	2: 41,231,861 (GRCm39)	H1203R	probably benign	Het
Lrrc8a	C	T	2: 30,146,661 (GRCm39)	R492W	probably damaging	Het
Magel2	T	A	7: 62,030,342 (GRCm39)	V1082D	unknown	Het
Memo1	A	C	17: 74,552,049 (GRCm39)	H82Q	probably null	Het
Myh13	A	T	11: 67,252,115 (GRCm39)	T1408S	probably benign	Het
Myh2	A	T	11: 67,085,451 (GRCm39)	N1792Y	possibly damaging	Het
Myo1e	A	T	9: 70,275,969 (GRCm39)	N728I	possibly damaging	Het
Myo1e	T	C	9: 70,285,997 (GRCm39)		probably benign	Het
Myo5c	T	C	9: 75,196,337 (GRCm39)		probably benign	Het
Or11l3	T	A	11: 58,516,319 (GRCm39)	L184F	probably damaging	Het
Or1e19	A	G	11: 73,316,188 (GRCm39)	V207A	probably benign	Het
Or2d2b	T	C	7: 106,705,643 (GRCm39)	I142V	probably benign	Het
Or4c11c	T	A	2: 88,661,749 (GRCm39)	M96K	possibly damaging	Het
Or51g1	T	A	7: 102,633,478 (GRCm39)	T298S	probably damaging	Het
Or52e3	T	C	7: 102,868,967 (GRCm39)	F14S	probably damaging	Het
Parp2	C	T	14: 51,047,543 (GRCm39)	A18V	probably benign	Het
Peli1	T	A	11: 21,098,110 (GRCm39)	C282S	probably damaging	Het
Phf8-ps	G	T	17: 33,286,598 (GRCm39)	S68*	probably null	Het
Piezo2	T	C	18: 63,252,006 (GRCm39)	M404V	possibly damaging	Het
Pkn1	T	A	8: 84,404,592 (GRCm39)	Q496L	possibly damaging	Het
Pla2r1	A	T	2: 60,262,317 (GRCm39)	F1093L	probably damaging	Het
Ppp2r3d	A	G	9: 101,022,680 (GRCm39)	V323A	probably damaging	Het
Pramel16	T	A	4: 143,676,453 (GRCm39)	Y217F	probably benign	Het
Prg2	C	T	2: 84,812,342 (GRCm39)		probably benign	Het
Ptprb	G	A	10: 116,182,958 (GRCm39)	G1545S	probably benign	Het
Rbm19	A	G	5: 120,258,307 (GRCm39)	D174G	possibly damaging	Het
Rhbdf2	T	A	11: 116,491,974 (GRCm39)	T526S	probably damaging	Het
Rpusd4	A	G	9: 35,179,310 (GRCm39)	N42S	probably benign	Het
Ryr3	T	A	2: 112,477,361 (GRCm39)	Q4455L	possibly damaging	Het
Sema4a	G	T	3: 88,358,668 (GRCm39)	H30Q	probably damaging	Het
Slc1a3	A	G	15: 8,675,153 (GRCm39)	V284A	probably benign	Het
Slc30a9	A	T	5: 67,497,318 (GRCm39)	K288*	probably null	Het
Slc36a1	G	T	11: 55,119,164 (GRCm39)	A380S	probably benign	Het
Slc47a1	G	A	11: 61,268,833 (GRCm39)		probably benign	Het
Snx19	A	T	9: 30,340,296 (GRCm39)	E478V	probably benign	Het
Spag6	T	C	2: 18,738,916 (GRCm39)		probably benign	Het
Stag1	A	T	9: 100,668,740 (GRCm39)	T223S	probably damaging	Het
Terb1	A	T	8: 105,224,732 (GRCm39)		probably benign	Het
Terf1	A	G	1: 15,876,170 (GRCm39)	D90G	possibly damaging	Het
Tex15	A	G	8: 34,061,302 (GRCm39)	D518G	probably damaging	Het
Tmem174	T	A	13: 98,773,546 (GRCm39)	M95L	possibly damaging	Het
Tnnt3	GTCCAGGCATCTC	GTC	7: 142,066,364 (GRCm39)		probably benign	Het
Usp28	A	G	9: 48,896,803 (GRCm39)	D8G	probably benign	Het
Vmn2r105	T	C	17: 20,444,840 (GRCm39)	T551A	probably damaging	Het
Vmn2r107	A	G	17: 20,595,549 (GRCm39)	I701V	probably benign	Het
Vmn2r13	A	C	5: 109,339,943 (GRCm39)	F11V	probably benign	Het
Vmn2r85	G	C	10: 130,261,443 (GRCm39)	S298*	probably null	Het
Wdr6	C	G	9: 108,452,554 (GRCm39)	W443S	probably damaging	Het
Wipi1	A	G	11: 109,474,016 (GRCm39)	V210A	probably damaging	Het
Zfp317	A	G	9: 19,556,532 (GRCm39)	T47A	probably benign	Het
Zfp61	T	C	7: 23,991,714 (GRCm39)	T146A	probably benign	Het
Zfp964	A	G	8: 70,116,567 (GRCm39)	E389G	unknown	Het
Zfyve16	T	C	13: 92,640,985 (GRCm39)	D1253G	probably damaging	Het
Zpld2	T	C	4: 133,929,669 (GRCm39)	K212R	possibly damaging	Het
Zswim7	G	A	11: 62,158,299 (GRCm39)		probably benign	Het

Other mutations in Skint1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00330:Skint1	APN	4	111,878,777 (GRCm39)	critical splice donor site	probably null
IGL01890:Skint1	APN	4	111,867,878 (GRCm39)	missense	probably damaging	1.00
IGL02020:Skint1	APN	4	111,882,724 (GRCm39)	missense	probably benign	0.08
IGL02045:Skint1	APN	4	111,882,727 (GRCm39)	missense	possibly damaging	0.80
R0421:Skint1	UTSW	4	111,876,211 (GRCm39)	missense	possibly damaging	0.74
R0544:Skint1	UTSW	4	111,878,562 (GRCm39)	missense	probably damaging	1.00
R0617:Skint1	UTSW	4	111,886,596 (GRCm39)	splice site	probably benign
R0881:Skint1	UTSW	4	111,886,054 (GRCm39)	missense	probably benign	0.04
R0973:Skint1	UTSW	4	111,885,412 (GRCm39)	splice site	probably benign
R1036:Skint1	UTSW	4	111,876,493 (GRCm39)	missense	possibly damaging	0.71
R1469:Skint1	UTSW	4	111,882,708 (GRCm39)	missense	probably benign	0.00
R1469:Skint1	UTSW	4	111,882,708 (GRCm39)	missense	probably benign	0.00
R2063:Skint1	UTSW	4	111,882,730 (GRCm39)	missense	probably benign	0.00
R2064:Skint1	UTSW	4	111,882,730 (GRCm39)	missense	probably benign	0.00
R2065:Skint1	UTSW	4	111,882,730 (GRCm39)	missense	probably benign	0.00
R2066:Skint1	UTSW	4	111,882,730 (GRCm39)	missense	probably benign	0.00
R2067:Skint1	UTSW	4	111,882,730 (GRCm39)	missense	probably benign	0.00
R2372:Skint1	UTSW	4	111,876,348 (GRCm39)	missense	probably damaging	1.00
R2518:Skint1	UTSW	4	111,882,678 (GRCm39)	missense	probably benign	0.25
R2971:Skint1	UTSW	4	111,878,527 (GRCm39)	missense	possibly damaging	0.50
R4656:Skint1	UTSW	4	111,878,674 (GRCm39)	missense	probably damaging	1.00
R4993:Skint1	UTSW	4	111,885,530 (GRCm39)	critical splice donor site	probably null
R5083:Skint1	UTSW	4	111,886,630 (GRCm39)	missense	probably benign	0.01
R5450:Skint1	UTSW	4	111,882,729 (GRCm39)	missense	probably benign	0.00
R5583:Skint1	UTSW	4	111,876,253 (GRCm39)	missense	probably damaging	1.00
R5645:Skint1	UTSW	4	111,882,699 (GRCm39)	missense	probably benign	0.41
R5877:Skint1	UTSW	4	111,878,720 (GRCm39)	nonsense	probably null
R5950:Skint1	UTSW	4	111,876,532 (GRCm39)	missense	probably benign
R5974:Skint1	UTSW	4	111,876,516 (GRCm39)	missense	probably benign	0.02
R6216:Skint1	UTSW	4	111,878,679 (GRCm39)	missense	probably benign	0.00
R6494:Skint1	UTSW	4	111,867,909 (GRCm39)	missense	probably benign	0.06
R7348:Skint1	UTSW	4	111,878,770 (GRCm39)	missense	probably damaging	1.00
R7752:Skint1	UTSW	4	111,876,399 (GRCm39)	missense	probably damaging	1.00
R7901:Skint1	UTSW	4	111,876,399 (GRCm39)	missense	probably damaging	1.00
R8515:Skint1	UTSW	4	111,867,921 (GRCm39)	missense	probably benign	0.10
R9417:Skint1	UTSW	4	111,878,509 (GRCm39)	missense	probably benign	0.33

Predicted Primers

PCR Primer
(F):5'- TGCAATTAGAGCCCTTACCTCTTTAG -3'
(R):5'- TAGAGCTTAAGCAATCAAGTCAAGG -3'

Sequencing Primer
(F):5'- GTTTTACTCTTCTGTTCCAACCAG -3'
(R):5'- GTCAAGGAAGAAAATGAATCATTCTG -3'

Posted On

2014-08-25