Mutagenetix > Incidental Mutation

Incidental Mutation 'RF009:Csnk1d'

603076

Institutional Source

Beutler Lab

Gene Symbol

Csnk1d

Ensembl Gene

ENSMUSG00000025162

Gene Name

casein kinase 1, delta

Synonyms

1200006A05Rik

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

RF009 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

120849816-120882156 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 120862453 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 275 (N275K)

Ref Sequence

ENSEMBL: ENSMUSP00000018274 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000018274] [ENSMUST00000070575]

AlphaFold

Q9DC28

PDB Structure

A P21 crystal form of mammalian casein kinase 1 delta [X-RAY DIFFRACTION]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000018274
AA Change: N275K

PolyPhen 2 Score 0.811 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000018274
Gene: ENSMUSG00000025162
AA Change: N275K

Domain	Start	End	E-Value	Type
Pfam:Pkinase_Tyr	9	273	3.7e-18	PFAM
Pfam:Pkinase	9	277	1.8e-28	PFAM
low complexity region	299	314	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000070575
AA Change: N275K

PolyPhen 2 Score 0.806 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000070721
Gene: ENSMUSG00000025162
AA Change: N275K

Domain	Start	End	E-Value	Type
Pfam:Pkinase_Tyr	9	273	1.6e-18	PFAM
Pfam:Pkinase	9	280	2.8e-41	PFAM
low complexity region	299	314	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000146837

SMART Domains

Protein: ENSMUSP00000115055
Gene: ENSMUSG00000025162

Domain	Start	End	E-Value	Type
Pfam:Pkinase	2	55	6.6e-6	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000154483

SMART Domains

Protein: ENSMUSP00000117472
Gene: ENSMUSG00000025162

Domain	Start	End	E-Value	Type
low complexity region	12	25	N/A	INTRINSIC
Pfam:Pkinase_Tyr	27	210	2.5e-12	PFAM
Pfam:Pkinase	28	218	3.4e-21	PFAM

Coding Region Coverage

1x: 99.8%
3x: 99.7%
10x: 99.3%
20x: 98.5%

Validation Efficiency

96% (53/55)

MGI Phenotype

FUNCTION: This gene encodes a member of the casein kinase I (CKI) family of serine/threonine protein kinases. A highly similar human protein regulates an array of cellular processes by influencing the Wnt and hedgehog signaling pathways. The encoded protein may also be involved in the regulation of apoptosis, circadian rhythm, microtubule dynamics, chromosome segregation, and p53-mediated effects on growth. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous null mice die 1.5 to 5 days after birth and fetal weight is significantly smaller than controls. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6030445D17Rik	ACACACACCCGC	AC	4: 136,189,661 (GRCm39)		probably null	Het
AI182371	A	G	2: 34,979,209 (GRCm39)	V153A	possibly damaging	Het
AI837181	CGG	CGGTGG	19: 5,475,262 (GRCm39)		probably benign	Het
Ankhd1	GCGGCG	GCGGCGTCGGCG	18: 36,693,975 (GRCm39)		probably benign	Het
Apoc2	C	T	7: 19,405,767 (GRCm39)	M71I	probably benign	Het
Arhgap17	CTGTTGTTG	CTGTTG	7: 122,886,085 (GRCm39)		probably benign	Het
Atrn	C	A	2: 130,748,842 (GRCm39)	T121K	probably benign	Het
Btnl12	T	C	16: 37,674,841 (GRCm39)	D207G	probably benign	Het
Ccdc170	C	CCAG	10: 4,511,030 (GRCm39)		probably benign	Het
Cckbr	GCA	G	7: 105,083,893 (GRCm39)		probably null	Het
Cdk13	T	C	13: 17,978,329 (GRCm39)	D303G	unknown	Het
Cfap65	C	A	1: 74,944,806 (GRCm39)	R1477L	probably damaging	Het
Chd2	A	G	7: 73,169,410 (GRCm39)	S37P	possibly damaging	Het
Chga	AGC	AGCCGC	12: 102,527,679 (GRCm39)		probably benign	Het
Csf2rb2	T	C	15: 78,176,127 (GRCm39)	I259V	probably benign	Het
Dmxl1	A	C	18: 50,026,461 (GRCm39)	R1856S	probably damaging	Het
Dnah5	T	C	15: 28,204,165 (GRCm39)	V14A	probably benign	Het
Edc4	G	A	8: 106,615,812 (GRCm39)	S729N	probably benign	Het
Emilin3	T	C	2: 160,751,012 (GRCm39)	S246G	probably benign	Het
Epc2	T	G	2: 49,422,249 (GRCm39)		probably null	Het
Exoc6	T	A	19: 37,560,068 (GRCm39)	F101I	probably benign	Het
Fam171b	GCAGCA	GCAGCACCAGCA	2: 83,643,224 (GRCm39)		probably benign	Het
Fam81b	CTGTT	CTGTTGTT	13: 76,419,435 (GRCm39)		probably benign	Het
Flywch1	CTCACCCACTCCTGGTGT	CTCACCCACTCCTGGTGTGGGGAGGCTACGTAGTCACCCACTCCTGGTGT	17: 23,981,135 (GRCm39)		probably null	Het
Gab3	TTC	TTCCTC	X: 74,043,598 (GRCm39)		probably benign	Het
Gab3	CTT	CTTATT	X: 74,043,630 (GRCm39)		probably null	Het
Gabpa	C	A	16: 84,641,224 (GRCm39)	Q93K	probably benign	Het
Gabre	GGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCTGGCTCAGGCTC	GGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCTGGCTCAGGCTC	X: 71,314,318 (GRCm39)		probably benign	Het
Gabre	GGCTCA	GGCTCAAGCTCA	X: 71,314,319 (GRCm39)		probably benign	Het
H2-T3	TCCCGAAGAAC	TC	17: 36,500,294 (GRCm39)		probably benign	Het
Htr5a	A	G	5: 28,047,859 (GRCm39)	D138G	probably damaging	Het
Ifi207	G	A	1: 173,556,558 (GRCm39)	P727S	probably benign	Het
Ifna13	T	A	4: 88,562,145 (GRCm39)	S160C	probably damaging	Het
Kcnh8	G	A	17: 53,285,267 (GRCm39)	R1079H	probably benign	Het
Klri2	GGAG	GG	6: 129,710,737 (GRCm39)		probably null	Het
Lce1m	GTTGCTGCCACTG	GTTGCTGCCACTGTTGCTGCCACTG	3: 92,925,438 (GRCm39)		probably benign	Het
Lrch1	TTGGTGGTGCTGGTGG	TTGGTGG	14: 75,185,014 (GRCm39)		probably benign	Het
Lrch4	A	G	5: 137,635,805 (GRCm39)		probably null	Het
Lrrc2	TTGATTCGGTTCACC	T	9: 110,810,744 (GRCm39)		probably null	Het
Map1a	GCTCCAGC	GCTCCAGCCCCAGCTCCAGCTCCAGCTCCACCTCCAGC	2: 121,136,782 (GRCm39)		probably benign	Het
Mettl25	T	C	10: 105,669,100 (GRCm39)		probably benign	Het
Mex3b	A	G	7: 82,516,968 (GRCm39)	D37G	probably damaging	Het
Mon1a	T	A	9: 107,778,433 (GRCm39)	V219E	probably damaging	Het
Myh3	TTACG	TTACGTACG	11: 66,977,183 (GRCm39)		probably null	Het
Myh3	GATTA	GATTAATTA	11: 66,977,181 (GRCm39)		probably null	Het
Myh3	ATTAC	ATTACTTAC	11: 66,977,182 (GRCm39)		probably null	Het
Myo5b	T	A	18: 74,777,070 (GRCm39)	C377S	probably damaging	Het
Nefh	ACTTGGCCTCAGCTGGGG	ACTTGGCCTCAGCTGGGGCCTTGGCCTCAGCTGGGG	11: 4,890,997 (GRCm39)		probably benign	Het
Nos1ap	T	C	1: 170,146,150 (GRCm39)	D468G	probably damaging	Het
Ntn5	T	C	7: 45,342,684 (GRCm39)		probably null	Het
Oog2	T	C	4: 143,921,855 (GRCm39)	V255A	probably benign	Het
Or5ac15	T	A	16: 58,940,274 (GRCm39)	H53L	probably damaging	Het
Or8b37	A	T	9: 37,959,043 (GRCm39)	H175L	probably damaging	Het
Pdgfd	C	A	9: 6,288,624 (GRCm39)	L93M	probably damaging	Het
Pgls	G	T	8: 72,045,107 (GRCm39)	V83L	probably damaging	Het
Pigw	C	A	11: 84,767,987 (GRCm39)	Q447H	probably damaging	Het
Pnma8a	TCATGATGCACCTGCTTCAACATC	TCATGATGCACCTGCTTCAACATCGCATGATGCACCTGCTTCAACATC	7: 16,695,352 (GRCm39)		probably benign	Het
Poc1a	C	A	9: 106,172,417 (GRCm39)	L253M	possibly damaging	Het
Ppl	T	A	16: 4,915,795 (GRCm39)	E589D	probably benign	Het
Prkar1b	A	G	5: 139,094,376 (GRCm39)	S71P	probably benign	Het
Prx	T	C	7: 27,218,385 (GRCm39)	F1101S	probably damaging	Het
Rffl	A	G	11: 82,736,598 (GRCm39)	V26A	probably benign	Het
Scube3	T	A	17: 28,387,371 (GRCm39)	L923Q	probably damaging	Het
Setd2	C	T	9: 110,379,779 (GRCm39)	P1198L	probably damaging	Het
Shank2	C	A	7: 143,965,308 (GRCm39)	A972E	possibly damaging	Het
Slc10a6	A	G	5: 103,756,858 (GRCm39)	L302P	probably damaging	Het
Slc29a3	C	T	10: 60,586,340 (GRCm39)	G42D	probably benign	Het
Spart	T	C	3: 55,035,027 (GRCm39)	V471A	probably benign	Het
Srebf1	T	C	11: 60,094,942 (GRCm39)	T486A	probably benign	Het
Sspo	T	A	6: 48,436,919 (GRCm39)	Y1284*	probably null	Het
Supt20	AGCAGC	AGCAGCCGCAGC	3: 54,635,083 (GRCm39)		probably benign	Het
Tcof1	GCA	GCACCA	18: 60,968,815 (GRCm39)		probably benign	Het
Tff1	CTTCCTG	C	17: 31,383,901 (GRCm39)		probably benign	Het
Tmprss13	ATCTCCAGCAAGGGCACCTCCTCAGGCCTCTCCAGCAAGGACACCTCCTCAGGCCTCTCCAACAAGGACACCTCCTCAGGCCTCTCCAGCAAGGGCACCTCCTC	ATCTCCAGCAAGGGCACCTCCTCAGGGCTCTCCAGCAAGGGCACCTCCTCAGGCCTCTCCAGCAAGGACACCTCCTCAGGCCTCTCCAACAAGGACACCTCCTCAGGCCTCTCCAGCAAGGGCACCTCCTC	9: 45,239,762 (GRCm39)		probably benign	Het
Tnfrsf25	T	C	4: 152,204,081 (GRCm39)	W341R	probably damaging	Het
Trappc9	GCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT	GCTGCTGCTGCTGCTTCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT	15: 72,673,136 (GRCm39)		probably benign	Het
Trav8d-1	T	A	14: 53,016,207 (GRCm39)	L31Q	probably damaging	Het
Ttc23	A	T	7: 67,375,777 (GRCm39)	I452F	possibly damaging	Het
Uimc1	T	C	13: 55,198,598 (GRCm39)	E526G	possibly damaging	Het
Ulbp1	T	A	10: 7,397,405 (GRCm39)	K233N	unknown	Het
Usp17ld	A	T	7: 102,899,495 (GRCm39)	V479E	probably damaging	Het
Utrn	T	TGTTACCC	10: 12,509,689 (GRCm39)		probably null	Het
Vmn1r9	C	T	6: 57,048,465 (GRCm39)	S180L	probably benign	Het
Wdr97	GAGGAGGA	G	15: 76,247,367 (GRCm39)		probably null	Het
Zfp598	CACC	CACCCCTACC	17: 24,899,761 (GRCm39)		probably benign	Het

Other mutations in Csnk1d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01689:Csnk1d	APN	11	120,862,393 (GRCm39)	missense	probably benign	0.06
IGL01905:Csnk1d	APN	11	120,864,789 (GRCm39)	missense	probably damaging	1.00
IGL02476:Csnk1d	APN	11	120,863,338 (GRCm39)	missense	probably damaging	1.00
R1971:Csnk1d	UTSW	11	120,863,274 (GRCm39)	missense	possibly damaging	0.95
R2245:Csnk1d	UTSW	11	120,863,229 (GRCm39)	missense	probably damaging	1.00
R4472:Csnk1d	UTSW	11	120,855,800 (GRCm39)	unclassified	probably benign
R4767:Csnk1d	UTSW	11	120,859,954 (GRCm39)	missense	probably benign
R4809:Csnk1d	UTSW	11	120,854,668 (GRCm39)	unclassified	probably benign
R4870:Csnk1d	UTSW	11	120,874,014 (GRCm39)	intron	probably benign
R6522:Csnk1d	UTSW	11	120,862,449 (GRCm39)	missense	probably damaging	1.00
R6657:Csnk1d	UTSW	11	120,855,820 (GRCm39)	missense	possibly damaging	0.75

Predicted Primers

PCR Primer
(F):5'- CTTGCAAACCCGAGTCTTGC -3'
(R):5'- CTCCCAAAGGCCAGATATGACTAG -3'

Sequencing Primer
(F):5'- GCAGACAGCAAAGCTTTACATACAG -3'
(R):5'- GGCCAGATATGACTAGTCTTCAG -3'

Posted On

2019-12-04