Mutagenetix > Incidental Mutation

Incidental Mutation 'PIT4469001:Psd4'

555817

Institutional Source

Beutler Lab

Gene Symbol

Psd4

Ensembl Gene

ENSMUSG00000026979

Gene Name

pleckstrin and Sec7 domain containing 4

Synonyms

SEC7 homolog, EFA6B

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

PIT4469001 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

24257571-24299882 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 24284306 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Asparagine at position 57 (D57N)

Ref Sequence

ENSEMBL: ENSMUSP00000062415 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056641] [ENSMUST00000102942] [ENSMUST00000127242] [ENSMUST00000131930] [ENSMUST00000140547] [ENSMUST00000142522] [ENSMUST00000166388]

AlphaFold

Q8BLR5

Predicted Effect

probably benign
Transcript: ENSMUST00000056641
AA Change: D57N

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000062415
Gene: ENSMUSG00000026979
AA Change: D57N

Domain	Start	End	E-Value	Type
low complexity region	156	176	N/A	INTRINSIC
low complexity region	350	361	N/A	INTRINSIC
low complexity region	420	438	N/A	INTRINSIC
low complexity region	458	474	N/A	INTRINSIC
Sec7	497	688	9.39e-47	SMART
PH	727	843	1.1e-10	SMART
low complexity region	883	893	N/A	INTRINSIC
low complexity region	897	920	N/A	INTRINSIC
low complexity region	961	973	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000102942
AA Change: D57N

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000100006
Gene: ENSMUSG00000026979
AA Change: D57N

Domain	Start	End	E-Value	Type
low complexity region	156	176	N/A	INTRINSIC
low complexity region	350	361	N/A	INTRINSIC
low complexity region	420	438	N/A	INTRINSIC
low complexity region	458	474	N/A	INTRINSIC
Sec7	497	688	9.39e-47	SMART
PH	727	843	1.1e-10	SMART
low complexity region	883	893	N/A	INTRINSIC
low complexity region	897	920	N/A	INTRINSIC
low complexity region	961	973	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000127242
AA Change: D57N

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)

Predicted Effect

probably benign
Transcript: ENSMUST00000131930
AA Change: D57N

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)

Predicted Effect

probably benign
Transcript: ENSMUST00000140547

Predicted Effect

probably benign
Transcript: ENSMUST00000142522
AA Change: D57N

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)

Predicted Effect

probably benign
Transcript: ENSMUST00000166388
AA Change: D57N

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000132395
Gene: ENSMUSG00000026979
AA Change: D57N

Domain	Start	End	E-Value	Type
low complexity region	156	176	N/A	INTRINSIC
low complexity region	350	361	N/A	INTRINSIC
low complexity region	420	438	N/A	INTRINSIC
low complexity region	458	474	N/A	INTRINSIC
Sec7	497	688	9.39e-47	SMART
PH	727	843	1.1e-10	SMART
low complexity region	883	893	N/A	INTRINSIC
low complexity region	897	920	N/A	INTRINSIC
low complexity region	961	973	N/A	INTRINSIC

Coding Region Coverage

1x: 93.3%
3x: 90.7%
10x: 84.4%
20x: 71.1%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 29 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A630001G21Rik	A	G	1: 85,652,920 (GRCm39)	F83L	probably benign	Het
Acsm2	T	A	7: 119,177,408 (GRCm39)	C308S	possibly damaging	Het
Ak3	A	G	19: 29,025,157 (GRCm39)	S25P	probably damaging	Het
Atp13a2	T	A	4: 140,721,438 (GRCm39)	V176E	unknown	Het
Bmper	A	T	9: 23,317,845 (GRCm39)	H488L	probably benign	Het
Cacna1c	A	T	6: 118,572,933 (GRCm39)	C2084S	unknown	Het
Ccp110	T	A	7: 118,321,600 (GRCm39)	N418K	probably benign	Het
Ddx17	C	A	15: 79,428,014 (GRCm39)	G32C	probably damaging	Het
Dennd2b	G	A	7: 109,130,337 (GRCm39)	A888V	probably damaging	Het
Dusp16	G	A	6: 134,738,115 (GRCm39)		probably benign	Het
Efl1	T	G	7: 82,307,373 (GRCm39)	F90V	probably benign	Het
Ell2	T	A	13: 75,910,011 (GRCm39)	N252K	probably damaging	Het
Gdf6	T	C	4: 9,859,569 (GRCm39)	V217A	probably damaging	Het
H1f4	A	T	13: 23,806,362 (GRCm39)	V40E	probably damaging	Het
Hint1	T	A	11: 54,760,896 (GRCm39)	S112T	unknown	Het
Kif5c	T	C	2: 49,631,360 (GRCm39)	V679A	probably benign	Het
Lrrn3	A	T	12: 41,503,017 (GRCm39)	D433E	probably benign	Het
Mast4	G	A	13: 102,941,226 (GRCm39)	T277M	probably damaging	Het
Naa11	A	G	5: 97,539,485 (GRCm39)		probably null	Het
Pcdh18	T	A	3: 49,709,518 (GRCm39)	H599L	probably benign	Het
Pgc	A	T	17: 48,039,680 (GRCm39)	K25*	probably null	Het
Pramel58	T	A	5: 94,830,652 (GRCm39)	V50E	probably damaging	Het
Pxdn	G	A	12: 30,055,828 (GRCm39)	R1238Q	probably benign	Het
Smim41	T	C	15: 101,191,152 (GRCm39)	V6A	probably benign	Het
Spata32	T	C	11: 103,100,653 (GRCm39)	N38S	probably benign	Het
Tpr	A	G	1: 150,279,707 (GRCm39)	T279A	probably benign	Het
Unc13a	C	A	8: 72,110,958 (GRCm39)	E418*	probably null	Het
Vmn2r97	C	A	17: 19,149,878 (GRCm39)	T422K	probably benign	Het
Zfp474	A	T	18: 52,771,791 (GRCm39)	Q148L	possibly damaging	Het

Other mutations in Psd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00850:Psd4	APN	2	24,284,298 (GRCm39)	missense	probably benign	0.25
IGL01302:Psd4	APN	2	24,286,799 (GRCm39)	critical splice donor site	probably null
IGL01446:Psd4	APN	2	24,295,407 (GRCm39)	missense	probably damaging	1.00
IGL01577:Psd4	APN	2	24,293,234 (GRCm39)	missense	probably damaging	0.96
IGL01823:Psd4	APN	2	24,284,444 (GRCm39)	missense	probably benign	0.27
IGL02103:Psd4	APN	2	24,290,540 (GRCm39)	nonsense	probably null
IGL02212:Psd4	APN	2	24,295,326 (GRCm39)	nonsense	probably null
IGL02240:Psd4	APN	2	24,286,389 (GRCm39)	missense	probably benign	0.00
IGL02261:Psd4	APN	2	24,291,756 (GRCm39)	missense	probably damaging	1.00
IGL02345:Psd4	APN	2	24,291,835 (GRCm39)	critical splice donor site	probably null
IGL03272:Psd4	APN	2	24,295,692 (GRCm39)	splice site	probably benign
bitcoin	UTSW	2	24,291,569 (GRCm39)	missense	probably damaging	1.00
crypto	UTSW	2	24,287,259 (GRCm39)	missense	probably benign
Ethereum	UTSW	2	24,296,996 (GRCm39)	missense	probably damaging	1.00
underworld	UTSW	2	24,295,363 (GRCm39)	missense	probably damaging	1.00
R0131:Psd4	UTSW	2	24,295,363 (GRCm39)	missense	probably damaging	1.00
R0131:Psd4	UTSW	2	24,295,363 (GRCm39)	missense	probably damaging	1.00
R0132:Psd4	UTSW	2	24,295,363 (GRCm39)	missense	probably damaging	1.00
R0278:Psd4	UTSW	2	24,284,450 (GRCm39)	missense	probably damaging	1.00
R1303:Psd4	UTSW	2	24,285,030 (GRCm39)	missense	probably benign	0.00
R1551:Psd4	UTSW	2	24,293,292 (GRCm39)	missense	probably benign	0.02
R1715:Psd4	UTSW	2	24,295,344 (GRCm39)	missense	probably damaging	1.00
R1854:Psd4	UTSW	2	24,287,468 (GRCm39)	missense	probably benign	0.26
R1942:Psd4	UTSW	2	24,295,805 (GRCm39)	missense	probably damaging	1.00
R2392:Psd4	UTSW	2	24,284,679 (GRCm39)	missense	probably damaging	0.98
R2420:Psd4	UTSW	2	24,291,253 (GRCm39)	missense	probably damaging	1.00
R4509:Psd4	UTSW	2	24,286,347 (GRCm39)	missense	probably benign
R4512:Psd4	UTSW	2	24,292,901 (GRCm39)	missense	probably damaging	1.00
R4558:Psd4	UTSW	2	24,294,806 (GRCm39)	missense	probably damaging	1.00
R4995:Psd4	UTSW	2	24,287,259 (GRCm39)	missense	probably benign
R5120:Psd4	UTSW	2	24,295,450 (GRCm39)	missense	probably benign
R5314:Psd4	UTSW	2	24,290,528 (GRCm39)	missense	possibly damaging	0.89
R5563:Psd4	UTSW	2	24,284,897 (GRCm39)	missense	probably benign
R5638:Psd4	UTSW	2	24,287,427 (GRCm39)	missense	probably benign	0.14
R6191:Psd4	UTSW	2	24,284,499 (GRCm39)	missense	probably damaging	1.00
R6224:Psd4	UTSW	2	24,291,569 (GRCm39)	missense	probably damaging	1.00
R7024:Psd4	UTSW	2	24,284,555 (GRCm39)	missense	possibly damaging	0.76
R7046:Psd4	UTSW	2	24,284,985 (GRCm39)	missense	probably benign	0.05
R7209:Psd4	UTSW	2	24,287,357 (GRCm39)	missense	probably damaging	1.00
R7483:Psd4	UTSW	2	24,294,768 (GRCm39)	missense	possibly damaging	0.65
R7498:Psd4	UTSW	2	24,296,996 (GRCm39)	missense	probably damaging	1.00
R7571:Psd4	UTSW	2	24,297,023 (GRCm39)	missense	probably damaging	1.00
R7741:Psd4	UTSW	2	24,291,108 (GRCm39)	critical splice donor site	probably null
R7978:Psd4	UTSW	2	24,294,867 (GRCm39)	missense	probably damaging	1.00
R8133:Psd4	UTSW	2	24,286,701 (GRCm39)	missense	probably benign
R8254:Psd4	UTSW	2	24,293,223 (GRCm39)	missense	probably damaging	0.99
R8786:Psd4	UTSW	2	24,295,444 (GRCm39)	missense	probably benign	0.08
R8797:Psd4	UTSW	2	24,287,440 (GRCm39)	missense	probably benign	0.02
R9015:Psd4	UTSW	2	24,287,492 (GRCm39)	missense
R9413:Psd4	UTSW	2	24,287,472 (GRCm39)	missense	probably benign	0.39
X0009:Psd4	UTSW	2	24,291,537 (GRCm39)	missense	probably damaging	1.00
X0064:Psd4	UTSW	2	24,294,750 (GRCm39)	missense	probably damaging	0.99
Z1177:Psd4	UTSW	2	24,284,943 (GRCm39)	frame shift	probably null
Z1177:Psd4	UTSW	2	24,284,924 (GRCm39)	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- CAGATGCTACCAAGGGCTTCTG -3'
(R):5'- AGGTCCAGGACACACATCTG -3'

Sequencing Primer
(F):5'- CAACCATCACTCTGTGGATGATG -3'
(R):5'- AGGACACACATCTGGGCCTG -3'

Posted On

2019-06-07