Mutagenetix > Incidental Mutation

Incidental Mutation 'R4982:Phtf1'

384895

Institutional Source

Beutler Lab

Gene Symbol

Phtf1

Ensembl Gene

ENSMUSG00000058388

Gene Name

putative homeodomain transcription factor 1

Synonyms

Phft

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4982 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

103968110-104024598 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 103998708 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 524 (S524T)

Ref Sequence

ENSEMBL: ENSMUSP00000088184 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000055425] [ENSMUST00000063717] [ENSMUST00000090685] [ENSMUST00000117150] [ENSMUST00000145727] [ENSMUST00000150849]

AlphaFold

Q9QZ09

Predicted Effect

probably damaging
Transcript: ENSMUST00000055425
AA Change: S516T

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000058137
Gene: ENSMUSG00000058388
AA Change: S516T

Domain	Start	End	E-Value	Type
Pfam:Phtf-FEM1B_bdg	3	60	8.6e-31	PFAM
Pfam:Phtf-FEM1B_bdg	57	105	5.2e-18	PFAM
low complexity region	117	128	N/A	INTRINSIC
low complexity region	294	317	N/A	INTRINSIC
transmembrane domain	470	492	N/A	INTRINSIC
transmembrane domain	557	579	N/A	INTRINSIC
transmembrane domain	594	611	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000063717
AA Change: S569T

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000066607
Gene: ENSMUSG00000058388
AA Change: S569T

Domain	Start	End	E-Value	Type
Pfam:Phtf-FEM1B_bdg	5	151	9.9e-73	PFAM
low complexity region	155	163	N/A	INTRINSIC
low complexity region	170	181	N/A	INTRINSIC
low complexity region	347	370	N/A	INTRINSIC
transmembrane domain	473	492	N/A	INTRINSIC
transmembrane domain	512	534	N/A	INTRINSIC
transmembrane domain	610	632	N/A	INTRINSIC
transmembrane domain	647	664	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000090685
AA Change: S524T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000088184
Gene: ENSMUSG00000058388
AA Change: S524T

Domain	Start	End	E-Value	Type
Pfam:Phtf-FEM1B_bdg	3	158	8.9e-89	PFAM
low complexity region	302	325	N/A	INTRINSIC
transmembrane domain	428	447	N/A	INTRINSIC
transmembrane domain	467	489	N/A	INTRINSIC
transmembrane domain	565	587	N/A	INTRINSIC
transmembrane domain	602	619	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000117150
AA Change: S569T

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000113973
Gene: ENSMUSG00000058388
AA Change: S569T

Domain	Start	End	E-Value	Type
Pfam:Phtf-FEM1B_bdg	3	158	1.6e-88	PFAM
low complexity region	170	181	N/A	INTRINSIC
low complexity region	347	370	N/A	INTRINSIC
transmembrane domain	473	492	N/A	INTRINSIC
transmembrane domain	512	534	N/A	INTRINSIC
transmembrane domain	610	632	N/A	INTRINSIC
transmembrane domain	647	664	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130385

Predicted Effect

probably damaging
Transcript: ENSMUST00000145727
AA Change: S569T

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000114722
Gene: ENSMUSG00000058388
AA Change: S569T

Domain	Start	End	E-Value	Type
Pfam:Phtf-FEM1B_bdg	3	158	1.6e-88	PFAM
low complexity region	170	181	N/A	INTRINSIC
low complexity region	347	370	N/A	INTRINSIC
transmembrane domain	473	492	N/A	INTRINSIC
transmembrane domain	512	534	N/A	INTRINSIC
transmembrane domain	610	632	N/A	INTRINSIC
transmembrane domain	647	664	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150090

Predicted Effect

probably benign
Transcript: ENSMUST00000150849

SMART Domains

Protein: ENSMUSP00000118281
Gene: ENSMUSG00000058388

Domain	Start	End	E-Value	Type
Pfam:Phtf-FEM1B_bdg	3	158	4.5e-90	PFAM
low complexity region	170	181	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.1%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	A	T	11: 9,292,348	I1404L	possibly damaging	Het
Adra1b	A	G	11: 43,835,230	S287P	probably damaging	Het
Atxn2	G	T	5: 121,814,343	A1280S	possibly damaging	Het
Bbip1	T	C	19: 53,932,208		probably null	Het
Bbs2	A	G	8: 94,082,354		probably null	Het
Bcl11b	A	T	12: 107,965,772	C180*	probably null	Het
Bod1l	A	G	5: 41,820,473	V1166A	probably benign	Het
Bora	C	T	14: 99,047,352	P13S	probably damaging	Het
C2cd4c	T	C	10: 79,613,241	E24G	probably benign	Het
Ccne1	A	T	7: 38,100,571	I196N	probably damaging	Het
Chsy3	C	T	18: 59,409,575	S595L	probably benign	Het
Chsy3	T	A	18: 59,409,767	I659N	possibly damaging	Het
Cntrob	T	A	11: 69,311,362		probably null	Het
Col5a2	G	A	1: 45,389,458	P983S	possibly damaging	Het
Crat	T	A	2: 30,407,136		probably null	Het
Ctnnbl1	C	T	2: 157,836,553	H359Y	probably benign	Het
D430041D05Rik	A	G	2: 104,255,387	V83A	possibly damaging	Het
Dixdc1	A	G	9: 50,682,602	S488P	possibly damaging	Het
Dmrta1	T	C	4: 89,688,564	C86R	probably damaging	Het
Dnase1l1	C	T	X: 74,277,038		probably null	Homo
Fam171a1	G	A	2: 3,178,468		probably null	Het
Fam222b	T	C	11: 78,154,743	C249R	probably damaging	Het
Fbxw18	T	A	9: 109,702,651		probably benign	Het
Fes	T	C	7: 80,387,204	Y44C	probably damaging	Het
Gimap6	A	G	6: 48,707,999	V51A	probably benign	Het
Gpr75	C	A	11: 30,891,462	H122Q	probably damaging	Het
Gpr75	C	T	11: 30,891,463	L123F	possibly damaging	Het
Greb1	A	G	12: 16,724,761	S212P	probably damaging	Het
Grin3a	T	C	4: 49,665,512	H1041R	probably benign	Het
Ifna5	A	G	4: 88,835,624	N34D	probably damaging	Het
Ift140	A	T	17: 25,036,994	H221L	probably damaging	Het
Igsf3	T	C	3: 101,435,667	V540A	probably benign	Het
Il10ra	A	G	9: 45,269,059	L5S	probably damaging	Het
Klra2	A	T	6: 131,220,189	D282E	probably benign	Het
Lyst	T	A	13: 13,725,954	H3138Q	probably damaging	Het
Malrd1	A	G	2: 16,042,129	T1689A	probably benign	Het
Mon2	A	T	10: 122,995,789	L1671M	probably damaging	Het
Mpped1	T	C	15: 83,836,327	F71S	probably damaging	Het
Mtpap	C	A	18: 4,396,332	H541Q	probably benign	Het
Muc5ac	T	A	7: 141,809,456		probably benign	Het
Mybbp1a	T	C	11: 72,445,214	I451T	probably damaging	Het
Myh7	T	A	14: 54,972,767	E1827V	probably damaging	Het
Olfr132	A	T	17: 38,130,577	I205N	probably damaging	Het
Olfr145	C	A	9: 37,897,515	T37N	probably damaging	Het
Olfr342	A	T	2: 36,527,397		probably null	Het
Olfr501-ps1	T	A	7: 108,508,648	Y197*	probably null	Het
Os9	C	T	10: 127,121,051	R23H	possibly damaging	Het
Otud6b	A	G	4: 14,815,607	L261P	probably damaging	Het
Pcdhga2	A	G	18: 37,669,423	N107D	probably benign	Het
Pclo	C	T	5: 14,679,294		probably benign	Het
Peg10	T	TCCG	6: 4,756,451		probably benign	Het
Pkdrej	A	C	15: 85,818,996	L913R	probably damaging	Het
Pld1	C	A	3: 28,031,298	A201D	probably damaging	Het
Rorb	T	A	19: 18,977,688	Q103L	probably benign	Het
Sec24d	C	T	3: 123,299,606	T284M	probably benign	Het
Serpinb3b	T	C	1: 107,157,754	I86V	probably benign	Het
Serpinb6a	A	T	13: 33,918,874	M201K	probably damaging	Het
Snx8	A	G	5: 140,352,234	S219P	probably benign	Het
Sp8	C	T	12: 118,848,425	T5I	probably damaging	Het
Tanc1	A	G	2: 59,799,943	N749D	probably damaging	Het
Tarm1	G	C	7: 3,489,096	P284A	probably damaging	Het
Tbx15	A	T	3: 99,254,074	E65V	probably benign	Het
Ticam1	T	A	17: 56,272,020	H25L	probably benign	Het
Tmprss11g	T	A	5: 86,492,815	L170F	probably damaging	Het
Tnfsf9	A	G	17: 57,107,504	*310W	probably null	Het
Tsks	C	T	7: 44,943,994	T128I	possibly damaging	Het
Uhrf1bp1	T	C	17: 27,886,606	F702S	probably benign	Het
Vmn1r175	A	T	7: 23,809,069	N44K	possibly damaging	Het
Vmn1r45	A	G	6: 89,933,865	I41T	probably damaging	Het
Ythdc2	A	G	18: 44,871,465	N1102S	probably benign	Het
Zswim4	C	T	8: 84,226,667		probably null	Het

Other mutations in Phtf1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00809:Phtf1	APN	3	103988667	missense	probably benign
IGL01139:Phtf1	APN	3	104005602	missense	probably damaging	1.00
IGL01677:Phtf1	APN	3	103998783	missense	probably damaging	1.00
IGL02169:Phtf1	APN	3	103997499	missense	probably benign
IGL02542:Phtf1	APN	3	103993906	splice site	probably benign
IGL02557:Phtf1	APN	3	103998765	missense	probably damaging	1.00
IGL02697:Phtf1	APN	3	103997563	missense	probably benign
IGL02807:Phtf1	APN	3	103997553	missense	probably benign	0.00
R0140:Phtf1	UTSW	3	103987560	missense	probably null	1.00
R0555:Phtf1	UTSW	3	104004469	missense	probably damaging	1.00
R0620:Phtf1	UTSW	3	103993765	missense	probably damaging	1.00
R1480:Phtf1	UTSW	3	103987434	nonsense	probably null
R1799:Phtf1	UTSW	3	103996642	missense	probably benign	0.01
R1804:Phtf1	UTSW	3	103987567	unclassified	probably benign
R1921:Phtf1	UTSW	3	103969122	nonsense	probably null
R1943:Phtf1	UTSW	3	103993882	nonsense	probably null
R2006:Phtf1	UTSW	3	104004483	critical splice donor site	probably null
R3729:Phtf1	UTSW	3	103985779	missense	probably benign	0.00
R3731:Phtf1	UTSW	3	103985779	missense	probably benign	0.00
R4051:Phtf1	UTSW	3	104005508	missense	possibly damaging	0.92
R4210:Phtf1	UTSW	3	104003603	critical splice donor site	probably null
R4211:Phtf1	UTSW	3	104003603	critical splice donor site	probably null
R4730:Phtf1	UTSW	3	103987435	missense	probably damaging	1.00
R5314:Phtf1	UTSW	3	103999287	missense	probably damaging	1.00
R5321:Phtf1	UTSW	3	104003511	missense	probably benign	0.31
R5499:Phtf1	UTSW	3	103991175	missense	probably benign	0.00
R6134:Phtf1	UTSW	3	104004405	missense	probably damaging	0.99
R6603:Phtf1	UTSW	3	103993873	missense	probably damaging	1.00
R7242:Phtf1	UTSW	3	103998696	missense	probably damaging	0.99
R7311:Phtf1	UTSW	3	103997664	missense	possibly damaging	0.64
R7519:Phtf1	UTSW	3	103969119	missense	probably damaging	1.00
R7601:Phtf1	UTSW	3	103993845	missense	probably benign	0.03
R7657:Phtf1	UTSW	3	103969113	missense	probably benign	0.00
R8354:Phtf1	UTSW	3	104004449	missense	probably damaging	1.00
R8454:Phtf1	UTSW	3	104004449	missense	probably damaging	1.00
R8669:Phtf1	UTSW	3	104003476	missense	probably benign	0.39
R9020:Phtf1	UTSW	3	103991378	nonsense	probably null
R9295:Phtf1	UTSW	3	103997577	missense	probably benign	0.00
R9682:Phtf1	UTSW	3	103993898	missense	possibly damaging	0.86
R9798:Phtf1	UTSW	3	103997553	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- GGGTGGACTTTGACATGAACAC -3'
(R):5'- TCATTTCCCAGTGACCACAG -3'

Sequencing Primer
(F):5'- GGACTTTGACATGAACACTGCTG -3'
(R):5'- GCCACTCTGCAACTCTAGC -3'

Posted On

2016-05-10