Mutagenetix > Incidental Mutation

Incidental Mutation 'R1954:Clp1'

217539

Institutional Source

Beutler Lab

Gene Symbol

Clp1

Ensembl Gene

ENSMUSG00000027079

Gene Name

CLP1, cleavage and polyadenylation factor I subunit

Synonyms

MMRRC Submission

039968-MU

Accession Numbers

Genbank: NM_133840; MGI: 2138968

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R1954 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

84722104-84727350 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 84724051 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 258 (D258G)

Ref Sequence

ENSEMBL: ENSMUSP00000129300 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028475] [ENSMUST00000165219]

AlphaFold

Q99LI9

Predicted Effect

probably damaging
Transcript: ENSMUST00000028475
AA Change: D258G

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

SMART Domains

Protein: ENSMUSP00000028475
Gene: ENSMUSG00000027079
AA Change: D258G

Domain	Start	End	E-Value	Type
Pfam:CLP1_N	15	107	1.7e-36	PFAM
Pfam:CLP1_P	121	307	2e-79	PFAM
Pfam:Clp1	312	423	1.3e-34	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138231

Predicted Effect

probably damaging
Transcript: ENSMUST00000165219
AA Change: D258G

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

SMART Domains

Protein: ENSMUSP00000129300
Gene: ENSMUSG00000027079
AA Change: D258G

Domain	Start	End	E-Value	Type
low complexity region	15	28	N/A	INTRINSIC
Pfam:MobB	115	230	5.7e-24	PFAM
Pfam:Clp1	232	424	3e-62	PFAM

Meta Mutation Damage Score

0.4233

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.0%

Validation Efficiency

97% (101/104)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the Clp1 family. The encoded protein is a multifunctional kinase which is a component of the tRNA splicing endonuclease complex and a component of the pre-mRNA cleavage complex II. This protein is implicated in tRNA, mRNA, and siRNA maturation. Mutations in this gene are associated with pontocerebellar hypoplasia type 10 (PCH10). Alternatively splice transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]
PHENOTYPE: Mice homozygous for a kinase dead allele exhibit background sensitive lethality, motor neuron degeneration, defects in diaphragm innervation, progressive muscle weakness and impaired pre-tRNA processing. Mice homozygous for a globally targeted allele exhibit complete embryonic lethality. [provided by MGI curators]

Allele List at MGI

All alleles(6) : Gene trapped(6)

Other mutations in this stock

Total: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700007G11Rik	A	T	5: 98,566,753		probably benign	Het
Adamts15	T	A	9: 30,910,708	M478L	probably benign	Het
Akap8l	T	A	17: 32,336,736	Y123F	possibly damaging	Het
Anapc4	T	G	5: 52,846,625		probably benign	Het
Arap3	A	G	18: 37,982,002	V987A	probably damaging	Het
Atp2b4	T	A	1: 133,739,992	T105S	probably damaging	Het
Atp6v0d1	A	G	8: 105,565,893	L7P	probably damaging	Het
Atp6v1b2	T	C	8: 69,105,903	V341A	possibly damaging	Het
Baz2b	C	A	2: 59,968,743	A346S	probably benign	Het
Brpf3	G	A	17: 28,806,559	S202N	probably benign	Het
Btnl4	T	C	17: 34,472,930	K233E	possibly damaging	Het
Capn7	A	G	14: 31,360,150	T438A	probably damaging	Het
Cars2	A	T	8: 11,550,286	Y68N	probably damaging	Het
Cbx2	G	T	11: 119,028,340	G244W	probably damaging	Het
Ccr4	A	T	9: 114,492,685	V104D	probably damaging	Het
Cdc5l	T	C	17: 45,426,516		probably null	Het
Cep170	A	T	1: 176,756,384	C810S	probably benign	Het
Clstn3	T	C	6: 124,459,298	E164G	possibly damaging	Het
Col28a1	T	C	6: 7,998,516	E1131G	probably damaging	Het
Cps1	A	G	1: 67,195,196	D914G	possibly damaging	Het
Ctnnal1	C	T	4: 56,817,242		probably benign	Het
Cyp2c38	A	G	19: 39,404,687	L312P	probably damaging	Het
Cytip	T	C	2: 58,148,253	N99D	possibly damaging	Het
Dennd4a	A	T	9: 64,852,467	T285S	probably benign	Het
Dhx8	A	G	11: 101,753,279	S842G	probably damaging	Het
Disp1	A	T	1: 183,088,543	M771K	probably damaging	Het
Dnah17	A	G	11: 118,024,731	I4326T	probably damaging	Het
Efcab7	T	C	4: 99,900,690	F345L	probably damaging	Het
Erc1	G	T	6: 119,797,305	Q230K	probably damaging	Het
Ern1	A	T	11: 106,421,974		probably benign	Het
Espl1	T	C	15: 102,298,388	Y96H	probably damaging	Het
Fam135a	A	T	1: 24,029,602	L533I	probably damaging	Het
Fat2	G	A	11: 55,311,084	T388I	probably benign	Het
Galnt1	T	G	18: 24,271,774		probably benign	Het
Glmn	A	G	5: 107,572,377	F212S	probably damaging	Het
Gm3604	A	T	13: 62,369,211	N444K	probably damaging	Het
Gm5434	A	G	12: 36,090,596		probably benign	Het
Gm8989	A	C	7: 106,329,681	D336E	probably damaging	Het
H2-M10.3	T	C	17: 36,367,498	D145G	probably damaging	Het
Hic2	T	A	16: 17,258,993	L562Q	probably damaging	Het
Hip1r	G	T	5: 124,001,844	E1003D	probably damaging	Het
Hist1h1c	T	C	13: 23,739,402	V185A	unknown	Het
Hist1h1d	A	G	13: 23,555,516		probably benign	Het
Hsfy2	C	T	1: 56,637,183	C65Y	probably benign	Het
Inpp1	T	C	1: 52,794,629	T103A	probably damaging	Het
Ints5	T	C	19: 8,894,896	V73A	probably damaging	Het
Iqch	A	T	9: 63,548,016	D166E	probably benign	Het
Klhdc3	A	T	17: 46,677,975	N96K	probably damaging	Het
Klk1b8	C	T	7: 43,953,848		probably benign	Het
Klrb1	T	C	6: 128,723,073		probably null	Het
Krt71	C	A	15: 101,735,466	G446*	probably null	Het
Lars	G	A	18: 42,210,050	R1101C	probably damaging	Het
Lemd3	G	T	10: 120,978,940	S129R	probably damaging	Het
Lrp1b	A	G	2: 40,858,441	L3015P	probably damaging	Het
Mdga2	T	C	12: 66,486,708		probably benign	Het
Mlst8	A	T	17: 24,477,221	I178N	probably damaging	Het
Mon2	A	T	10: 123,038,483	I320N	probably damaging	Het
Morc2b	T	C	17: 33,137,490	Y436C	probably damaging	Het
Moxd1	T	A	10: 24,279,883	M295K	probably benign	Het
Mrps5	T	A	2: 127,596,897		probably null	Het
Mtor	C	A	4: 148,468,273	S744R	probably damaging	Het
Myo3a	T	A	2: 22,241,226	D61E	probably damaging	Het
Nars	C	T	18: 64,500,564	R545Q	probably damaging	Het
Ncoa6	A	G	2: 155,406,821	V1521A	possibly damaging	Het
Ndor1	T	C	2: 25,255,293	E20G	possibly damaging	Het
Nipsnap3b	T	C	4: 53,017,213		probably benign	Het
Notch3	G	T	17: 32,166,678	A39E	probably benign	Het
Olfr1336	G	T	7: 6,461,145	W212L	probably benign	Het
Olfr237-ps1	T	C	6: 43,153,977	I224T	possibly damaging	Het
Olfr345	A	G	2: 36,640,215	M59V	possibly damaging	Het
Otud3	T	C	4: 138,898,032	K237R	possibly damaging	Het
Papola	T	A	12: 105,828,273		probably null	Het
Parl	T	A	16: 20,302,327	M1L	possibly damaging	Het
Parp14	G	T	16: 35,858,301	N432K	probably benign	Het
Patz1	T	G	11: 3,291,088	S159A	probably damaging	Het
Prpf6	T	G	2: 181,632,077	M338R	probably benign	Het
Psd3	A	G	8: 67,697,075	L343P	probably damaging	Het
Ptpn23	A	T	9: 110,386,325	N1422K	probably damaging	Het
Rab19	A	T	6: 39,384,082	T55S	probably benign	Het
Sh3yl1	A	G	12: 30,922,333	K34E	possibly damaging	Het
Skint8	T	A	4: 111,950,081	F321L	possibly damaging	Het
Slc25a46	A	T	18: 31,600,241		probably null	Het
Slc26a3	T	C	12: 31,450,816	L184S	probably damaging	Het
Slc39a10	A	T	1: 46,835,174	S323T	possibly damaging	Het
Sorbs2	G	T	8: 45,745,738	R20L	probably benign	Het
Stk32a	A	T	18: 43,212,025	D13V	probably benign	Het
Tab2	T	C	10: 7,919,330	T463A	probably damaging	Het
Tenm2	T	A	11: 36,047,547	N1433I	possibly damaging	Het
Tmem200c	A	T	17: 68,840,961	I180F	probably damaging	Het
Tmem232	G	T	17: 65,484,487	H129N	probably benign	Het
Tmem242	T	C	17: 5,439,579	T47A	possibly damaging	Het
Ube2d1	A	T	10: 71,285,123	M1K	probably null	Het
Uckl1	T	C	2: 181,570,527	Q332R	probably benign	Het
Unc5b	T	C	10: 60,769,265		probably benign	Het
Vmn2r114	T	C	17: 23,311,112	Y107C	probably benign	Het
Vmn2r82	A	T	10: 79,396,056	S630C	probably damaging	Het
Wdr25	T	A	12: 108,898,541	V204E	probably damaging	Het
Xab2	T	A	8: 3,616,094	D227V	probably damaging	Het
Zfp286	A	G	11: 62,783,708	S104P	possibly damaging	Het
Zfp345	T	C	2: 150,474,821	D22G	probably damaging	Het

Other mutations in Clp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02725:Clp1	APN	2	84723864	missense	probably benign	0.36
D4186:Clp1	UTSW	2	84725635	missense	probably benign	0.00
R0540:Clp1	UTSW	2	84725591	missense	possibly damaging	0.69
R0607:Clp1	UTSW	2	84725591	missense	possibly damaging	0.69
R2908:Clp1	UTSW	2	84724144	missense	possibly damaging	0.89
R4769:Clp1	UTSW	2	84725875	missense	possibly damaging	0.53
R4949:Clp1	UTSW	2	84723742	missense	possibly damaging	0.58
R5568:Clp1	UTSW	2	84725978	nonsense	probably null
R7191:Clp1	UTSW	2	84724146	nonsense	probably null
R8341:Clp1	UTSW	2	84723773	missense	probably damaging	0.98
R9055:Clp1	UTSW	2	84723922	missense	probably damaging	1.00
R9220:Clp1	UTSW	2	84723732	missense	probably damaging	1.00
R9351:Clp1	UTSW	2	84723851	missense	probably benign	0.01
R9366:Clp1	UTSW	2	84726129	missense	probably benign
Z1177:Clp1	UTSW	2	84725963	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- TCCTGAGACATACCCAGAGG -3'
(R):5'- TCCAGATTACATCTCGCTTAGC -3'

Sequencing Primer
(F):5'- CATCAGAAAATTTGACGTTGAAGGC -3'
(R):5'- ACATCTCGCTTAGCAGATGTG -3'

Posted On

2014-08-01