Mutagenetix > Incidental Mutation

Incidental Mutation 'R4902:Psmd4'

377862

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

042505-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4902 (G1)

Quality Score

224

Status

Validated

Chromosome

Chromosomal Location

94939999-94949880 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 94943170 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 78 (V78A)

Ref Sequence

ENSEMBL: ENSMUSP00000113554 (fasta)

Gene Model

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

AlphaFold

O35226

Predicted Effect

probably damaging
Transcript: ENSMUST00000071664
AA Change: V78A

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000071589
Gene: ENSMUSG00000005625
AA Change: V78A

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 damaging
Transcript: ENSMUST00000107237
AA Change: V78A

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000102857
Gene: ENSMUSG00000005625
AA Change: V78A

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 damaging
Transcript: ENSMUST00000117355
AA Change: V78A

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000113554
Gene: ENSMUSG00000005625
AA Change: V78A

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

probably benign
Transcript: ENSMUST00000140348

SMART Domains

Protein: ENSMUSP00000114545
Gene: ENSMUSG00000005625

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

0.1493

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 95.9%
20x: 91.0%

Validation Efficiency

100% (84/84)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930488N24Rik	T	C	17: 14,326,408 (GRCm39)		noncoding transcript	Het
Adamdec1	T	C	14: 68,809,215 (GRCm39)	N249S	probably damaging	Het
Asxl1	T	A	2: 153,241,751 (GRCm39)	V767E	probably benign	Het
Atp6v1f	T	C	6: 29,470,271 (GRCm39)		probably benign	Het
Brix1	T	C	15: 10,483,378 (GRCm39)		probably null	Het
Cap2	T	C	13: 46,684,501 (GRCm39)	V2A	probably damaging	Het
Chrnb2	A	G	3: 89,668,248 (GRCm39)	C356R	probably damaging	Het
Chtf8	C	T	8: 107,612,424 (GRCm39)	G172R	probably damaging	Het
Cybb	C	G	X: 9,316,989 (GRCm39)	D246H	probably benign	Het
Dact2	T	A	17: 14,416,991 (GRCm39)	K403M	possibly damaging	Het
Dhx40	A	C	11: 86,662,036 (GRCm39)	L674V	possibly damaging	Het
Dlc1	A	G	8: 37,044,285 (GRCm39)	V1230A	probably damaging	Het
Dnah7b	T	A	1: 46,329,935 (GRCm39)	S3260T	probably benign	Het
Eef1a2	T	A	2: 180,789,881 (GRCm39)	D428V	probably benign	Het
Ehd1	T	C	19: 6,344,273 (GRCm39)	F178L	possibly damaging	Het
Eif4a3l1	T	G	6: 136,306,262 (GRCm39)	V241G	probably benign	Het
F2	A	T	2: 91,465,316 (GRCm39)		probably benign	Het
Fam186a	T	C	15: 99,844,723 (GRCm39)	D507G	unknown	Het
Fbxo11	G	A	17: 88,372,702 (GRCm39)		probably benign	Het
Fry	A	T	5: 150,419,168 (GRCm39)	M2871L	probably benign	Het
Gabrr2	A	G	4: 33,095,512 (GRCm39)	D442G	probably damaging	Het
Gemin5	A	G	11: 58,055,103 (GRCm39)	I214T	probably benign	Het
Gfra2	A	G	14: 71,204,455 (GRCm39)	N175S	probably damaging	Het
Gprc5c	G	T	11: 114,755,093 (GRCm39)	V257L	possibly damaging	Het
Jhy	C	T	9: 40,808,821 (GRCm39)		probably benign	Het
Krtap5-5	A	T	7: 141,783,156 (GRCm39)	C165S	unknown	Het
Lce1k	T	A	3: 92,714,134 (GRCm39)	T17S	unknown	Het
Map3k1	C	T	13: 111,909,146 (GRCm39)	R268Q	probably damaging	Het
Med13l	T	A	5: 118,883,195 (GRCm39)	H1351Q	probably damaging	Het
Met	T	C	6: 17,546,995 (GRCm39)	V876A	probably damaging	Het
Mical2	T	C	7: 111,936,107 (GRCm39)	S903P	probably benign	Het
Mkks	A	G	2: 136,718,094 (GRCm39)	V396A	probably benign	Het
Mvk	T	C	5: 114,594,060 (GRCm39)	V305A	probably benign	Het
Myo5a	A	G	9: 75,081,360 (GRCm39)	T982A	probably benign	Het
N4bp1	A	G	8: 87,588,311 (GRCm39)	V209A	probably benign	Het
Nfkbib	G	T	7: 28,461,173 (GRCm39)	S158*	probably null	Het
Nkx3-1	G	A	14: 69,428,367 (GRCm39)	G72S	probably benign	Het
Ogfr	A	G	2: 180,235,518 (GRCm39)		probably benign	Het
Or10a3	G	A	7: 108,480,624 (GRCm39)	T63I	probably benign	Het
Or2t43	G	A	11: 58,457,451 (GRCm39)	S240F	possibly damaging	Het
Or8s8	T	C	15: 98,354,796 (GRCm39)	S202P	probably damaging	Het
Pcdhga8	T	A	18: 37,948,978 (GRCm39)	D131E	probably damaging	Het
Plch1	A	G	3: 63,648,264 (GRCm39)		probably benign	Het
Polrmt	A	G	10: 79,582,385 (GRCm39)	M1T	probably null	Het
Ppp1r12a	T	C	10: 108,066,451 (GRCm39)	V214A	probably damaging	Het
Prr5l	A	G	2: 101,628,027 (GRCm39)		probably benign	Het
Prss35	A	G	9: 86,638,175 (GRCm39)	Q315R	probably damaging	Het
Psg29	G	T	7: 16,945,837 (GRCm39)	*469L	probably null	Het
Rad9a	C	A	19: 4,251,552 (GRCm39)		probably benign	Het
Rfx7	G	T	9: 72,524,573 (GRCm39)	V588F	probably benign	Het
Rnase13	A	C	14: 52,160,052 (GRCm39)	I29S	probably benign	Het
Steap2	T	C	5: 5,725,866 (GRCm39)	N386S	possibly damaging	Het
Ston1	A	G	17: 88,952,680 (GRCm39)	E719G	probably damaging	Het
Stx4a	A	G	7: 127,441,934 (GRCm39)		probably null	Het
Tekt2	A	G	4: 126,217,263 (GRCm39)	S212P	possibly damaging	Het
Tex19.2	A	T	11: 121,007,782 (GRCm39)	L222Q	probably damaging	Het
Tmem50a	A	G	4: 134,637,017 (GRCm39)	I38T	probably damaging	Het
Ubr2	A	G	17: 47,296,922 (GRCm39)	V286A	possibly damaging	Het
Ugt2b35	T	C	5: 87,151,159 (GRCm39)	M255T	possibly damaging	Het
Vmn2r17	T	A	5: 109,601,220 (GRCm39)	F839L	probably benign	Het
Wdr36	T	C	18: 32,992,314 (GRCm39)	V617A	possibly damaging	Het
Wtip	A	T	7: 33,818,437 (GRCm39)		probably null	Het
Yeats2	G	A	16: 20,026,418 (GRCm39)	G765S	probably benign	Het
Zbtb3	T	C	19: 8,781,331 (GRCm39)	S315P	probably benign	Het
Zdhhc8	T	C	16: 18,045,030 (GRCm39)	M259V	probably benign	Het
Zfp120	A	G	2: 149,961,440 (GRCm39)		probably benign	Het
Zfp236	A	T	18: 82,627,543 (GRCm39)	I1552N	possibly damaging	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
R5090:Psmd4	UTSW	3	94,942,559 (GRCm39)	missense	possibly damaging	0.53
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'- TCCTTTCTATACTGAGTAAGCACCC -3'
(R):5'- AGTTGCTTTTAAGGTCTCTAAACAA -3'

Sequencing Primer
(F):5'- TGAGTAAGCACCCTCTAGATCAGTG -3'
(R):5'- CTTTAGTCTCAGCACTCGGGAG -3'

Posted On

2016-04-15