Mutagenetix > Incidental Mutation

Incidental Mutation 'R1555:Phyhd1'

170206

Institutional Source

Beutler Lab

Gene Symbol

Phyhd1

Ensembl Gene

ENSMUSG00000079484

Gene Name

phytanoyl-CoA dioxygenase domain containing 1

Synonyms

MMRRC Submission

039594-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.668) question?

Stock #

R1555 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

30156215-30172161 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 30164718 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 100 (I100N)

Ref Sequence

ENSEMBL: ENSMUSP00000116062 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000091132] [ENSMUST00000113643] [ENSMUST00000113645] [ENSMUST00000127689] [ENSMUST00000133877] [ENSMUST00000150695] [ENSMUST00000154647] [ENSMUST00000138254] [ENSMUST00000139719] [ENSMUST00000139454]

AlphaFold

Q9DB26

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000085290

Predicted Effect

probably damaging
Transcript: ENSMUST00000091132
AA Change: I120N

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000088663
Gene: ENSMUSG00000079484
AA Change: I120N

Domain	Start	End	E-Value	Type
Pfam:PhyH	32	279	2.7e-72	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000113643
AA Change: I100N

PolyPhen 2 Score 0.878 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000109273
Gene: ENSMUSG00000079484
AA Change: I100N

Domain	Start	End	E-Value	Type
Pfam:PhyH	12	238	9e-63	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000113645
AA Change: I100N

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000109275
Gene: ENSMUSG00000079484
AA Change: I100N

Domain	Start	End	E-Value	Type
Pfam:PhyH	12	259	1.4e-73	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000127689
AA Change: I100N

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000119543
Gene: ENSMUSG00000079484
AA Change: I100N

Domain	Start	End	E-Value	Type
Pfam:PhyH	12	150	7.5e-25	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129512

Predicted Effect

probably damaging
Transcript: ENSMUST00000133877
AA Change: I96N

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000117643
Gene: ENSMUSG00000079484
AA Change: I96N

Domain	Start	End	E-Value	Type
Pfam:PhyH	8	249	9.3e-70	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000150695
AA Change: I100N

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000121995
Gene: ENSMUSG00000079484
AA Change: I100N

Domain	Start	End	E-Value	Type
Pfam:PhyH	12	107	1.1e-16	PFAM
Pfam:PhyH	104	212	7.2e-40	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000154647
AA Change: I100N

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000121371
Gene: ENSMUSG00000079484
AA Change: I100N

Domain	Start	End	E-Value	Type
Pfam:PhyH	12	259	1.4e-73	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000138254
AA Change: I100N

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

SMART Domains

Protein: ENSMUSP00000116062
Gene: ENSMUSG00000079484
AA Change: I100N

Domain	Start	End	E-Value	Type
Pfam:PhyH	12	157	2.2e-28	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000139719
AA Change: I100N

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000116450
Gene: ENSMUSG00000079484
AA Change: I100N

Domain	Start	End	E-Value	Type
Pfam:PhyH	12	217	4.5e-57	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154988

Predicted Effect

probably benign
Transcript: ENSMUST00000139454

SMART Domains

Protein: ENSMUSP00000139038
Gene: ENSMUSG00000099041

Domain	Start	End	E-Value	Type
Pfam:DUF3733	1	65	3.3e-32	PFAM
Pfam:DUF3733	97	156	2e-22	PFAM
transmembrane domain	320	342	N/A	INTRINSIC
low complexity region	445	455	N/A	INTRINSIC
internal_repeat_1	461	526	7.6e-5	PROSPERO
low complexity region	540	558	N/A	INTRINSIC
LRR	590	613	5.41e0	SMART
LRR	614	636	3.18e2	SMART
LRR	638	660	6.78e1	SMART
LRR_TYP	661	684	1.06e-4	SMART
LRR	685	706	1.15e1	SMART
LRR_TYP	707	730	1.92e-2	SMART
LRR	731	751	1.81e2	SMART
LRR	753	776	2.02e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000147204

SMART Domains

Protein: ENSMUSP00000122095
Gene: ENSMUSG00000079484

Domain	Start	End	E-Value	Type
PDB:3OBZ\|A	2	42	4e-18	PDB

Meta Mutation Damage Score

0.9054

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.1%
20x: 92.0%

Validation Efficiency

96% (43/45)

Allele List at MGI

Other mutations in this stock

Total: 38 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ace	A	G	11: 105,865,727 (GRCm39)		probably null	Het
Adamts1	T	A	16: 85,594,776 (GRCm39)	T358S	probably benign	Het
Ate1	A	T	7: 130,110,821 (GRCm39)	F169I	probably benign	Het
Cdkl4	T	A	17: 80,851,043 (GRCm39)		probably benign	Het
Clcnkb	T	C	4: 141,139,050 (GRCm39)		probably null	Het
Col6a4	C	T	9: 105,878,085 (GRCm39)	R1964Q	possibly damaging	Het
Dcakd	C	T	11: 102,891,039 (GRCm39)	V17I	probably damaging	Het
Dcdc5	T	G	2: 106,214,480 (GRCm39)		noncoding transcript	Het
Erc2	T	A	14: 27,733,622 (GRCm39)	D557E	probably damaging	Het
Grid2	A	T	6: 64,406,668 (GRCm39)	D676V	possibly damaging	Het
Hebp2	G	T	10: 18,420,163 (GRCm39)	T90K	possibly damaging	Het
Igkv10-96	C	T	6: 68,609,365 (GRCm39)		probably benign	Het
Mier3	T	A	13: 111,844,893 (GRCm39)	N248K	probably damaging	Het
Myo5b	A	T	18: 74,702,853 (GRCm39)	I15F	probably damaging	Het
Neurl3	A	G	1: 36,305,613 (GRCm39)	V198A	probably benign	Het
Notch2	C	A	3: 98,038,656 (GRCm39)	N1266K	possibly damaging	Het
Nup107	A	G	10: 117,587,395 (GRCm39)		probably benign	Het
Or52e8b	T	C	7: 104,673,729 (GRCm39)	I153V	probably benign	Het
Or6d14	A	T	6: 116,533,787 (GRCm39)	I134F	probably damaging	Het
Phf3	G	T	1: 30,844,958 (GRCm39)	H1334N	possibly damaging	Het
Rad21l	T	A	2: 151,500,348 (GRCm39)	T224S	probably benign	Het
Rxra	C	T	2: 27,638,690 (GRCm39)	A231V	probably benign	Het
Sac3d1	T	C	19: 6,168,435 (GRCm39)	D61G	probably damaging	Het
Sbf1	A	G	15: 89,189,279 (GRCm39)	Y481H	probably damaging	Het
Spg11	T	C	2: 121,927,858 (GRCm39)	E642G	probably damaging	Het
Spta1	A	G	1: 174,006,315 (GRCm39)	Y159C	probably damaging	Het
Sry	C	G	Y: 2,662,975 (GRCm39)	Q228H	unknown	Het
Tedc1	G	T	12: 113,120,117 (GRCm39)		probably benign	Het
Tmem200a	A	T	10: 25,869,782 (GRCm39)	D162E	probably damaging	Het
Tmprss11e	T	A	5: 86,863,447 (GRCm39)	Q206L	probably damaging	Het
Tpra1	A	G	6: 88,887,185 (GRCm39)	N175S	probably damaging	Het
Ttll10	T	C	4: 156,119,596 (GRCm39)	E601G	probably benign	Het
Ttll6	G	T	11: 96,036,408 (GRCm39)	D346Y	probably damaging	Het
U2surp	A	G	9: 95,348,630 (GRCm39)	V874A	probably damaging	Het
Vwa5b1	T	C	4: 138,332,788 (GRCm39)	K258R	probably benign	Het
Xkr6	A	G	14: 64,056,374 (GRCm39)	Y95C	unknown	Het
Zfp180	T	C	7: 23,800,999 (GRCm39)		probably benign	Het
Zfp90	A	G	8: 107,150,727 (GRCm39)	T147A	probably benign	Het

Other mutations in Phyhd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0271:Phyhd1	UTSW	2	30,159,834 (GRCm39)	missense	probably benign	0.02
R0525:Phyhd1	UTSW	2	30,171,040 (GRCm39)	missense	probably damaging	1.00
R0665:Phyhd1	UTSW	2	30,171,040 (GRCm39)	missense	probably damaging	1.00
R5568:Phyhd1	UTSW	2	30,167,022 (GRCm39)	missense	probably damaging	1.00
R5714:Phyhd1	UTSW	2	30,169,994 (GRCm39)	missense	probably damaging	1.00
R5763:Phyhd1	UTSW	2	30,169,983 (GRCm39)	missense	probably damaging	1.00
R6334:Phyhd1	UTSW	2	30,164,736 (GRCm39)	critical splice donor site	probably null
R6854:Phyhd1	UTSW	2	30,159,773 (GRCm39)	missense	possibly damaging	0.92
R7792:Phyhd1	UTSW	2	30,156,782 (GRCm39)	start codon destroyed	probably null
R8526:Phyhd1	UTSW	2	30,156,955 (GRCm39)	critical splice donor site	probably null
R9284:Phyhd1	UTSW	2	30,156,879 (GRCm39)	nonsense	probably null
R9429:Phyhd1	UTSW	2	30,156,917 (GRCm39)	missense	probably benign	0.23
R9663:Phyhd1	UTSW	2	30,171,070 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGCAGCGGTGACAAGATCCGATTC -3'
(R):5'- CAGTGATCAACATCAAGGGACGCAG -3'

Sequencing Primer
(F):5'- CCGATTCTTCTTTGAAAAAGGCG -3'
(R):5'- ccctagttgtcctggaactc -3'

Posted On

2014-04-13