Mutagenetix > Incidental Mutation

Incidental Mutation 'R5090:Psmd4'

387681

Institutional Source

Beutler Lab

Gene Symbol

Psmd4

Ensembl Gene

ENSMUSG00000005625

Gene Name

proteasome (prosome, macropain) 26S subunit, non-ATPase, 4

Synonyms

angiocidin, Mcb1, Af1, multiubiquitin-chain-binding protein

MMRRC Submission

042679-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5090 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

94939999-94949880 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 94942559 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 7 (N7S)

Ref Sequence

ENSEMBL: ENSMUSP00000114545 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000071664] [ENSMUST00000107237] [ENSMUST00000117355] [ENSMUST00000140348]

AlphaFold

O35226

Predicted Effect

probably benign
Transcript: ENSMUST00000071664
AA Change: N120S

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000071589
Gene: ENSMUSG00000005625
AA Change: N120S

Domain	Start	End	E-Value	Type
VWA	2	188	7.38e-12	SMART
low complexity region	189	201	N/A	INTRINSIC
UIM	211	230	2.04e0	SMART
UIM	285	304	1.49e-2	SMART
low complexity region	307	320	N/A	INTRINSIC
low complexity region	367	379	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000107237
AA Change: N120S

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000102857
Gene: ENSMUSG00000005625
AA Change: N120S

Domain	Start	End	E-Value	Type
VWA	2	188	7.38e-12	SMART
low complexity region	189	201	N/A	INTRINSIC
UIM	211	230	2.04e0	SMART
UIM	282	301	1.49e-2	SMART
low complexity region	304	317	N/A	INTRINSIC
low complexity region	364	376	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000117355
AA Change: N120S

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000113554
Gene: ENSMUSG00000005625
AA Change: N120S

Domain	Start	End	E-Value	Type
VWA	2	188	7.38e-12	SMART
low complexity region	189	201	N/A	INTRINSIC
UIM	211	230	2.04e0	SMART
UIM	285	304	1.49e-2	SMART
low complexity region	307	320	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136868

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140280

Predicted Effect

possibly damaging
Transcript: ENSMUST00000140348
AA Change: N7S

PolyPhen 2 Score 0.528 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000114545
Gene: ENSMUSG00000005625
AA Change: N7S

Domain	Start	End	E-Value	Type
Pfam:UIM	34	42	2.4e-3	PFAM
UIM	100	119	1.49e-2	SMART
low complexity region	122	135	N/A	INTRINSIC
low complexity region	182	194	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000143688

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147960

Meta Mutation Damage Score

0.0734

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.3%
20x: 92.2%

Validation Efficiency

99% (66/67)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes one of the non-ATPase subunits of the 19S regulator lid. Pseudogenes have been identified on chromosomes 10 and 21. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele exhibit embryonic lethality and abnormal embryogenesis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca15	A	G	7: 119,984,422 (GRCm39)	S1168G	probably damaging	Het
Acsf2	A	T	11: 94,462,095 (GRCm39)		probably null	Het
Ankk1	G	T	9: 49,333,063 (GRCm39)	S140R	probably damaging	Het
Ash1l	G	T	3: 88,960,184 (GRCm39)	K2305N	probably damaging	Het
Asnsd1	C	T	1: 53,391,563 (GRCm39)		probably benign	Het
Atxn7l1	T	C	12: 33,376,077 (GRCm39)	S51P	probably damaging	Het
Ccdc88c	A	G	12: 100,920,439 (GRCm39)	L394P	probably damaging	Het
Cd200r1	T	A	16: 44,609,924 (GRCm39)	S48T	possibly damaging	Het
Cemip	T	C	7: 83,591,343 (GRCm39)	E1243G	probably damaging	Het
Cep192	T	A	18: 67,993,617 (GRCm39)	H1977Q	possibly damaging	Het
Cep250	T	C	2: 155,818,324 (GRCm39)	L833P	probably damaging	Het
Chd9	C	A	8: 91,753,462 (GRCm39)	Y1818*	probably null	Het
Clca3a1	C	A	3: 144,443,633 (GRCm39)	V706L	probably benign	Het
Cntln	T	C	4: 84,865,830 (GRCm39)	V162A	probably damaging	Het
Col5a1	G	A	2: 27,908,614 (GRCm39)	W67*	probably null	Het
Cux1	T	A	5: 136,342,054 (GRCm39)	N446I	possibly damaging	Het
Dlg1	G	T	16: 31,656,902 (GRCm39)	G599W	probably damaging	Het
Dock7	C	T	4: 98,879,648 (GRCm39)	V969I	probably benign	Het
Ephb3	T	C	16: 21,033,237 (GRCm39)	C74R	probably damaging	Het
Fads6	T	A	11: 115,187,480 (GRCm39)	T72S	probably benign	Het
Fra10ac1	C	T	19: 38,202,873 (GRCm39)	R110Q	probably damaging	Het
Gdf3	T	A	6: 122,586,713 (GRCm39)	L71F	probably benign	Het
Gm6685	A	G	11: 28,289,253 (GRCm39)	Y188H	probably benign	Het
Gm6981	A	C	9: 51,914,142 (GRCm39)		noncoding transcript	Het
Gnpda1	T	C	18: 38,465,146 (GRCm39)	T157A	probably damaging	Het
Grap2	A	C	15: 80,522,683 (GRCm39)	N70H	possibly damaging	Het
Gvin3	T	A	7: 106,200,109 (GRCm39)		noncoding transcript	Het
Hdac5	G	A	11: 102,088,539 (GRCm39)	R887C	probably damaging	Het
Hectd3	T	A	4: 116,857,435 (GRCm39)		probably benign	Het
Hmgcr	T	C	13: 96,787,098 (GRCm39)	K162E	probably benign	Het
Inpp5e	A	T	2: 26,289,383 (GRCm39)		probably null	Het
Kifap3	A	G	1: 163,683,645 (GRCm39)	D442G	possibly damaging	Het
Lama3	A	G	18: 12,675,459 (GRCm39)	T1015A	possibly damaging	Het
Lcp2	T	A	11: 34,039,725 (GRCm39)	Y508*	probably null	Het
Map1b	G	T	13: 99,566,534 (GRCm39)	Y2062*	probably null	Het
Mipep	A	G	14: 61,039,748 (GRCm39)	D259G	possibly damaging	Het
Mmp2	T	C	8: 93,579,202 (GRCm39)	F97S	probably damaging	Het
Mrpl18	A	C	17: 13,132,697 (GRCm39)	M144R	probably damaging	Het
Nek9	A	G	12: 85,376,616 (GRCm39)		probably null	Het
Nmral1	A	T	16: 4,532,395 (GRCm39)	Y139N	probably damaging	Het
Notch4	T	C	17: 34,799,894 (GRCm39)	C952R	probably damaging	Het
Nsf	T	C	11: 103,801,404 (GRCm39)	N204D	probably benign	Het
P2rx4	A	T	5: 122,863,118 (GRCm39)	D197V	probably damaging	Het
Pak5	A	T	2: 135,929,338 (GRCm39)	I615N	probably damaging	Het
Parp10	T	C	15: 76,125,925 (GRCm39)	D421G	probably damaging	Het
Pcdha6	A	T	18: 37,101,770 (GRCm39)	D321V	probably benign	Het
Pkhd1	T	A	1: 20,270,981 (GRCm39)	I3191F	probably damaging	Het
Ptprq	A	G	10: 107,361,950 (GRCm39)	V2084A	probably damaging	Het
Rab3gap1	A	G	1: 127,843,415 (GRCm39)	E263G	probably benign	Het
Rbm5	A	G	9: 107,637,511 (GRCm39)		probably benign	Het
Sacs	T	C	14: 61,442,702 (GRCm39)	F1583L	probably damaging	Het
Sel1l3	G	T	5: 53,357,388 (GRCm39)	H201Q	probably benign	Het
Shoc1	T	C	4: 59,111,108 (GRCm39)	T55A	unknown	Het
Tdpoz3	T	A	3: 93,733,870 (GRCm39)	W182R	possibly damaging	Het
Trim55	A	G	3: 19,725,771 (GRCm39)	N313S	probably benign	Het
Usp17lb	A	T	7: 104,490,290 (GRCm39)	D212E	probably benign	Het
Xirp2	A	G	2: 67,355,814 (GRCm39)	E3525G	possibly damaging	Het
Zfp236	T	C	18: 82,637,006 (GRCm39)	T1379A	probably benign	Het
Zfp553	A	T	7: 126,834,659 (GRCm39)	E71D	probably damaging	Het
Znrf1	T	G	8: 112,265,035 (GRCm39)	F21V	probably benign	Het

Other mutations in Psmd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02396:Psmd4	APN	3	94,943,221 (GRCm39)	missense	probably damaging	1.00
R0173:Psmd4	UTSW	3	94,940,234 (GRCm39)	missense	probably damaging	1.00
R1962:Psmd4	UTSW	3	94,944,012 (GRCm39)	missense	possibly damaging	0.89
R2907:Psmd4	UTSW	3	94,941,273 (GRCm39)	missense	probably damaging	0.99
R3781:Psmd4	UTSW	3	94,944,039 (GRCm39)	missense	probably benign	0.09
R3783:Psmd4	UTSW	3	94,942,562 (GRCm39)	missense	possibly damaging	0.85
R4902:Psmd4	UTSW	3	94,943,170 (GRCm39)	missense	probably damaging	0.98
R8031:Psmd4	UTSW	3	94,943,203 (GRCm39)	missense	probably damaging	1.00
R9221:Psmd4	UTSW	3	94,942,604 (GRCm39)	missense	probably damaging	1.00
R9312:Psmd4	UTSW	3	94,940,729 (GRCm39)	missense	probably benign	0.00
R9428:Psmd4	UTSW	3	94,940,767 (GRCm39)	missense	probably benign	0.00
R9464:Psmd4	UTSW	3	94,940,735 (GRCm39)	missense	probably benign	0.02
X0024:Psmd4	UTSW	3	94,944,028 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGCCTCACAGACGCATACAG -3'
(R):5'- TGGTCCACTTGAGGCACAAC -3'

Sequencing Primer
(F):5'- GAAATTCAGCATCCTACCAAAGGTC -3'
(R):5'- CATGTACCGAGTGAGCATTATG -3'

Posted On

2016-06-06