Mutagenetix > Incidental Mutation

Incidental Mutation 'R0140:Phtf1'

22240

Institutional Source

Beutler Lab

Gene Symbol

Phtf1

Ensembl Gene

ENSMUSG00000058388

Gene Name

putative homeodomain transcription factor 1

Synonyms

Phft

MMRRC Submission

038425-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0140 (G1)

Quality Score

225

Status

Validated (trace)

Chromosome

Chromosomal Location

103875426-103914806 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 103894876 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Tryptophan at position 208 (R208W)

Ref Sequence

ENSEMBL: ENSMUSP00000113973 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000055425] [ENSMUST00000063717] [ENSMUST00000090685] [ENSMUST00000117150] [ENSMUST00000123611] [ENSMUST00000145727] [ENSMUST00000150849] [ENSMUST00000156262]

AlphaFold

Q9QZ09

Predicted Effect

probably null
Transcript: ENSMUST00000055425
AA Change: R155W

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

SMART Domains

Protein: ENSMUSP00000058137
Gene: ENSMUSG00000058388
AA Change: R155W

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 null
Transcript: ENSMUST00000063717
AA Change: R208W

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

SMART Domains

Protein: ENSMUSP00000066607
Gene: ENSMUSG00000058388
AA Change: R208W

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 benign
Transcript: ENSMUST00000090685

SMART Domains

Protein: ENSMUSP00000088184
Gene: ENSMUSG00000058388

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 null
Transcript: ENSMUST00000117150
AA Change: R208W

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

SMART Domains

Protein: ENSMUSP00000113973
Gene: ENSMUSG00000058388
AA Change: R208W

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

probably null
Transcript: ENSMUST00000123611
AA Change: R189W

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000116193
Gene: ENSMUSG00000058388
AA Change: R189W

Domain	Start	End	E-Value	Type
Pfam:Phtf-FEM1B_bdg	9	139	1.7e-67	PFAM
low complexity region	151	162	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000145727
AA Change: R208W

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

SMART Domains

Protein: ENSMUSP00000114722
Gene: ENSMUSG00000058388
AA Change: R208W

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 damaging
Transcript: ENSMUST00000150849
AA Change: R208W

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

SMART Domains

Protein: ENSMUSP00000118281
Gene: ENSMUSG00000058388
AA Change: R208W

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

Predicted Effect

probably null
Transcript: ENSMUST00000156262

SMART Domains

Protein: ENSMUSP00000121036
Gene: ENSMUSG00000058388

Domain	Start	End	E-Value	Type
Pfam:Phtf-FEM1B_bdg	3	60	1e-31	PFAM
Pfam:Phtf-FEM1B_bdg	57	105	7.2e-19	PFAM
low complexity region	117	128	N/A	INTRINSIC

Meta Mutation Damage Score

0.2949

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.6%
20x: 93.4%

Validation Efficiency

98% (79/81)

Allele List at MGI

Other mutations in this stock

Total: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010315B03Rik	T	C	9: 124,057,789 (GRCm39)		probably benign	Het
9330161L09Rik	T	C	12: 103,373,587 (GRCm39)		probably benign	Het
Abca2	T	G	2: 25,328,097 (GRCm39)		probably null	Het
Adgrf3	T	C	5: 30,401,379 (GRCm39)	K13R	probably benign	Het
Arhgap15	C	A	2: 44,212,779 (GRCm39)	F416L	probably damaging	Het
Arhgef26	C	G	3: 62,355,666 (GRCm39)	T746R	probably benign	Het
Aspm	C	T	1: 139,408,379 (GRCm39)	T2422I	probably benign	Het
Atp4a	C	G	7: 30,419,526 (GRCm39)	R659G	probably benign	Het
AY358078	T	A	14: 52,063,399 (GRCm39)	D348E	probably benign	Het
Blnk	A	T	19: 40,928,668 (GRCm39)	S285T	probably damaging	Het
Calr3	C	T	8: 73,188,732 (GRCm39)		probably benign	Het
Camsap2	A	T	1: 136,208,120 (GRCm39)	V1124D	probably benign	Het
Ccdc40	G	A	11: 119,155,125 (GRCm39)	G1122S	probably benign	Het
Ccdc69	C	A	11: 54,941,325 (GRCm39)	C196F	possibly damaging	Het
Cdhr3	T	G	12: 33,130,412 (GRCm39)	N141T	probably benign	Het
Cdk4	T	C	10: 126,900,214 (GRCm39)	V37A	probably damaging	Het
Celsr2	C	T	3: 108,305,249 (GRCm39)	R2110K	probably benign	Het
Clcn7	A	G	17: 25,372,728 (GRCm39)	Y437C	probably damaging	Het
Col6a6	A	G	9: 105,579,474 (GRCm39)	F1917S	probably damaging	Het
Cps1	T	G	1: 67,219,275 (GRCm39)	S872A	probably benign	Het
Crebbp	G	T	16: 3,935,363 (GRCm39)	T842N	probably damaging	Het
Dennd2d	G	A	3: 106,399,799 (GRCm39)	V234I	probably benign	Het
Fam227b	T	C	2: 125,966,523 (GRCm39)	M130V	possibly damaging	Het
Fbxw24	G	T	9: 109,434,482 (GRCm39)	L373I	possibly damaging	Het
Fubp3	T	C	2: 31,498,196 (GRCm39)	Y359H	probably damaging	Het
Gm19684	T	C	17: 36,438,319 (GRCm39)		probably benign	Het
Hrnr	C	T	3: 93,238,800 (GRCm39)	Q3013*	probably null	Het
Il12rb1	T	C	8: 71,272,415 (GRCm39)		probably benign	Het
Lepr	A	T	4: 101,625,264 (GRCm39)	D473V	probably damaging	Het
Myof	A	T	19: 37,940,004 (GRCm39)	Y820*	probably null	Het
Nfil3	G	A	13: 53,121,681 (GRCm39)	Q408*	probably null	Het
Nolc1	G	A	19: 46,069,817 (GRCm39)		probably benign	Het
Npbwr1	A	C	1: 5,986,840 (GRCm39)	Y225D	probably damaging	Het
Nrip3	T	C	7: 109,361,022 (GRCm39)		probably benign	Het
Ntrk1	A	C	3: 87,685,875 (GRCm39)	L749R	probably damaging	Het
Or10ag53	A	G	2: 87,082,969 (GRCm39)	I229M	probably damaging	Het
Or2b11	A	G	11: 59,461,804 (GRCm39)	L254P	probably damaging	Het
Or4c126	T	A	2: 89,824,463 (GRCm39)	V242D	probably damaging	Het
Or52a24	A	G	7: 103,381,349 (GRCm39)	D72G	probably damaging	Het
Or6c211	G	T	10: 129,505,557 (GRCm39)	T277N	probably damaging	Het
Paox	A	T	7: 139,713,971 (GRCm39)	T244S	probably damaging	Het
Pcdhb9	T	A	18: 37,536,014 (GRCm39)	D669E	possibly damaging	Het
Pggt1b	A	G	18: 46,391,150 (GRCm39)		probably null	Het
Phkg1	T	A	5: 129,893,449 (GRCm39)	I334F	probably benign	Het
Pnliprp2	A	T	19: 58,754,795 (GRCm39)	I280F	probably benign	Het
Pnma8a	A	G	7: 16,694,147 (GRCm39)	M1V	probably null	Het
Prcp	A	G	7: 92,577,819 (GRCm39)	T328A	probably damaging	Het
Pxdn	A	G	12: 30,032,753 (GRCm39)	E179G	probably benign	Het
Racgap1	A	T	15: 99,521,532 (GRCm39)	N541K	probably benign	Het
Rnf103	T	A	6: 71,486,315 (GRCm39)	F315L	possibly damaging	Het
Septin2	A	G	1: 93,429,361 (GRCm39)	R237G	probably damaging	Het
Setd6	T	A	8: 96,442,737 (GRCm39)	L58Q	probably damaging	Het
Sipa1l1	G	A	12: 82,442,974 (GRCm39)	V755I	probably damaging	Het
Slc16a12	G	T	19: 34,650,104 (GRCm39)		probably benign	Het
Slk	G	A	19: 47,610,774 (GRCm39)	D815N	probably damaging	Het
Stx1a	T	C	5: 135,074,439 (GRCm39)		probably benign	Het
Tbc1d15	T	A	10: 115,056,124 (GRCm39)	I283F	probably damaging	Het
Tenm4	T	C	7: 96,545,259 (GRCm39)	I2425T	possibly damaging	Het
Tle1	G	A	4: 72,038,422 (GRCm39)	H702Y	probably damaging	Het
Tmc6	A	G	11: 117,657,077 (GRCm39)		probably benign	Het
Tmem268	G	A	4: 63,496,096 (GRCm39)	R179H	possibly damaging	Het
Tmem9	A	G	1: 135,961,900 (GRCm39)	K165R	probably damaging	Het
Trpm6	A	G	19: 18,796,558 (GRCm39)		probably null	Het
Tufm	C	T	7: 126,089,003 (GRCm39)	P88S	probably damaging	Het
Ubqln1	A	G	13: 58,341,103 (GRCm39)	I216T	probably damaging	Het
Urad	T	G	5: 147,259,141 (GRCm39)	M1L	probably benign	Het
Utp6	A	G	11: 79,847,551 (GRCm39)		probably benign	Het
Vav2	C	T	2: 27,163,688 (GRCm39)		probably benign	Het
Vmn2r55	G	T	7: 12,402,104 (GRCm39)	Q395K	possibly damaging	Het
Wwox	T	G	8: 115,433,027 (GRCm39)	V231G	probably damaging	Het
Zfp646	T	A	7: 127,482,678 (GRCm39)	N1618K	probably benign	Het
Zzef1	G	A	11: 72,790,377 (GRCm39)	M2110I	possibly damaging	Het

Other mutations in Phtf1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00809:Phtf1	APN	3	103,895,983 (GRCm39)	missense	probably benign
IGL01139:Phtf1	APN	3	103,912,918 (GRCm39)	missense	probably damaging	1.00
IGL01677:Phtf1	APN	3	103,906,099 (GRCm39)	missense	probably damaging	1.00
IGL02169:Phtf1	APN	3	103,904,815 (GRCm39)	missense	probably benign
IGL02542:Phtf1	APN	3	103,901,222 (GRCm39)	splice site	probably benign
IGL02557:Phtf1	APN	3	103,906,081 (GRCm39)	missense	probably damaging	1.00
IGL02697:Phtf1	APN	3	103,904,879 (GRCm39)	missense	probably benign
IGL02807:Phtf1	APN	3	103,904,869 (GRCm39)	missense	probably benign	0.00
R0555:Phtf1	UTSW	3	103,911,785 (GRCm39)	missense	probably damaging	1.00
R0620:Phtf1	UTSW	3	103,901,081 (GRCm39)	missense	probably damaging	1.00
R1480:Phtf1	UTSW	3	103,894,750 (GRCm39)	nonsense	probably null
R1799:Phtf1	UTSW	3	103,903,958 (GRCm39)	missense	probably benign	0.01
R1804:Phtf1	UTSW	3	103,894,883 (GRCm39)	unclassified	probably benign
R1921:Phtf1	UTSW	3	103,876,438 (GRCm39)	nonsense	probably null
R1943:Phtf1	UTSW	3	103,901,198 (GRCm39)	nonsense	probably null
R2006:Phtf1	UTSW	3	103,911,799 (GRCm39)	critical splice donor site	probably null
R3729:Phtf1	UTSW	3	103,893,095 (GRCm39)	missense	probably benign	0.00
R3731:Phtf1	UTSW	3	103,893,095 (GRCm39)	missense	probably benign	0.00
R4051:Phtf1	UTSW	3	103,912,824 (GRCm39)	missense	possibly damaging	0.92
R4210:Phtf1	UTSW	3	103,910,919 (GRCm39)	critical splice donor site	probably null
R4211:Phtf1	UTSW	3	103,910,919 (GRCm39)	critical splice donor site	probably null
R4730:Phtf1	UTSW	3	103,894,751 (GRCm39)	missense	probably damaging	1.00
R4982:Phtf1	UTSW	3	103,906,024 (GRCm39)	missense	probably damaging	1.00
R5314:Phtf1	UTSW	3	103,906,603 (GRCm39)	missense	probably damaging	1.00
R5321:Phtf1	UTSW	3	103,910,827 (GRCm39)	missense	probably benign	0.31
R5499:Phtf1	UTSW	3	103,898,491 (GRCm39)	missense	probably benign	0.00
R6134:Phtf1	UTSW	3	103,911,721 (GRCm39)	missense	probably damaging	0.99
R6603:Phtf1	UTSW	3	103,901,189 (GRCm39)	missense	probably damaging	1.00
R7242:Phtf1	UTSW	3	103,906,012 (GRCm39)	missense	probably damaging	0.99
R7311:Phtf1	UTSW	3	103,904,980 (GRCm39)	missense	possibly damaging	0.64
R7519:Phtf1	UTSW	3	103,876,435 (GRCm39)	missense	probably damaging	1.00
R7601:Phtf1	UTSW	3	103,901,161 (GRCm39)	missense	probably benign	0.03
R7657:Phtf1	UTSW	3	103,876,429 (GRCm39)	missense	probably benign	0.00
R8354:Phtf1	UTSW	3	103,911,765 (GRCm39)	missense	probably damaging	1.00
R8454:Phtf1	UTSW	3	103,911,765 (GRCm39)	missense	probably damaging	1.00
R8669:Phtf1	UTSW	3	103,910,792 (GRCm39)	missense	probably benign	0.39
R9020:Phtf1	UTSW	3	103,898,694 (GRCm39)	nonsense	probably null
R9295:Phtf1	UTSW	3	103,904,893 (GRCm39)	missense	probably benign	0.00
R9682:Phtf1	UTSW	3	103,901,214 (GRCm39)	missense	possibly damaging	0.86
R9798:Phtf1	UTSW	3	103,904,869 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- GGCTCAAGGCCACACATTGAAACTC -3'
(R):5'- TGTCTATCCTATGGCCCACCAACAC -3'

Sequencing Primer
(F):5'- AGTCCTGTTCTGGACAGCC -3'
(R):5'- GTGTTAGCTCTAAGAGCCCC -3'

Posted On

2013-04-16