Mutagenetix > Incidental Mutation

Incidental Mutation 'R7263:Cdk5rap1'

564730

Institutional Source

Beutler Lab

Gene Symbol

Cdk5rap1

Ensembl Gene

ENSMUSG00000027487

Gene Name

CDK5 regulatory subunit associated protein 1

Synonyms

2310066P17Rik

MMRRC Submission

045388-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.348) question?

Stock #

R7263 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

154177300-154214930 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 154202652 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Tyrosine at position 193 (N193Y)

Ref Sequence

ENSEMBL: ENSMUSP00000028990 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028990] [ENSMUST00000109730] [ENSMUST00000109731]

AlphaFold

Q8BTW8

Predicted Effect

probably benign
Transcript: ENSMUST00000028990
AA Change: N193Y

PolyPhen 2 Score 0.117 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000028990
Gene: ENSMUSG00000027487
AA Change: N193Y

Domain	Start	End	E-Value	Type
Pfam:UPF0004	100	203	3.2e-31	PFAM
Elp3	247	486	4.83e-52	SMART
Pfam:TRAM	500	574	1.2e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000109730

SMART Domains

Protein: ENSMUSP00000105352
Gene: ENSMUSG00000027487

Domain	Start	End	E-Value	Type
Pfam:UPF0004	100	181	1.3e-24	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000109731
AA Change: N193Y

PolyPhen 2 Score 0.117 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000105353
Gene: ENSMUSG00000027487
AA Change: N193Y

Domain	Start	End	E-Value	Type
Pfam:UPF0004	100	203	1.1e-31	PFAM
Elp3	247	486	4.83e-52	SMART
Pfam:TRAM	500	574	1e-12	PFAM

Meta Mutation Damage Score

0.0873

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.4%

Validation Efficiency

96% (67/70)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a regulator of cyclin-dependent kinase 5 activity. This protein has also been reported to modify RNA by adding a methylthio-group and may thus have a dual function as an RNA methylthiotransferase and as an inhibitor of cyclin-dependent kinase 5 activity. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, May 2013]
PHENOTYPE: Mice homozygous for a null allele show deficient mitochondrial tRNA modification, reduced mitochondrial protein synthesis, defects in oxidative phosphorylation, high susceptibility to stress-induced mitochondrial remodeling, and accelerated myopathy and cardiac dysfunction under stressed conditions. [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
Abca4	C	A	3: 121,847,843 (GRCm39)	H55N	probably damaging	Het
Acan	G	T	7: 78,742,066 (GRCm39)	V488L	probably damaging	Het
Adam12	T	C	7: 133,521,240 (GRCm39)	E638G	possibly damaging	Het
Adamts20	T	A	15: 94,220,772 (GRCm39)	Q1387L	possibly damaging	Het
Adamts3	G	T	5: 89,825,601 (GRCm39)	D1079E	probably benign	Het
Barx1	G	T	13: 48,818,555 (GRCm39)	G93C	probably damaging	Het
Carmil2	C	T	8: 106,419,677 (GRCm39)	R828C	probably damaging	Het
Catsper4	TTCTC	TTC	4: 133,954,423 (GRCm39)		probably null	Het
Ccdc159	T	C	9: 21,843,007 (GRCm39)	M148T	probably benign	Het
Csnk1g2	G	A	10: 80,470,332 (GRCm39)	G15D	probably damaging	Het
Dach1	T	C	14: 98,406,295 (GRCm39)	S151G	probably benign	Het
Elf5	C	A	2: 103,269,645 (GRCm39)	N75K	probably benign	Het
Elp3	T	C	14: 65,802,782 (GRCm39)	D272G	probably damaging	Het
Epb41l1	T	A	2: 156,337,043 (GRCm39)		probably null	Het
Epha6	A	G	16: 59,596,028 (GRCm39)	Y888H	probably damaging	Het
Fibcd1	T	C	2: 31,707,222 (GRCm39)	Y345C	probably damaging	Het
Gjd3	C	T	11: 102,690,963 (GRCm39)	E347K	possibly damaging	Het
Gse1	A	G	8: 121,300,910 (GRCm39)	D892G	unknown	Het
Gtpbp6	A	T	5: 110,251,915 (GRCm39)	I506N	probably benign	Het
Hivep1	T	A	13: 42,311,668 (GRCm39)	F1303I	possibly damaging	Het
Il21r	A	G	7: 125,232,077 (GRCm39)	T502A	probably benign	Het
Ints1	T	C	5: 139,749,834 (GRCm39)	T997A	possibly damaging	Het
Invs	C	A	4: 48,396,381 (GRCm39)	N351K	probably damaging	Het
Iqcm	A	G	8: 76,489,701 (GRCm39)	T390A	probably benign	Het
Iqcn	A	G	8: 71,163,425 (GRCm39)	N873D	possibly damaging	Het
Kcnh4	C	T	11: 100,632,643 (GRCm39)	G948D	probably benign	Het
Kcnh7	T	A	2: 62,566,314 (GRCm39)		probably null	Het
Lrrc72	A	G	12: 36,258,611 (GRCm39)	V82A	probably damaging	Het
Macf1	A	T	4: 123,271,943 (GRCm39)	L6535Q	probably damaging	Het
Ncor2	G	C	5: 125,109,196 (GRCm39)	L585V		Het
Nipal2	G	C	15: 34,578,904 (GRCm39)	Y298*	probably null	Het
Nipsnap1	C	T	11: 4,832,960 (GRCm39)		probably benign	Het
Or12e1	T	A	2: 87,022,476 (GRCm39)	C148*	probably null	Het
Or4x12-ps1	T	C	2: 89,916,332 (GRCm39)	I158V	not run	Het
Or51g1	A	T	7: 102,633,524 (GRCm39)	Y282*	probably null	Het
Pcdhga4	C	T	18: 37,819,873 (GRCm39)	T474I	probably benign	Het
Pdp1	G	T	4: 11,960,821 (GRCm39)	Q516K	possibly damaging	Het
Pik3c2b	C	T	1: 133,017,940 (GRCm39)	P934L	probably damaging	Het
Pp2d1	A	G	17: 53,822,358 (GRCm39)	I236T	probably benign	Het
Pygm	G	A	19: 6,438,357 (GRCm39)	R278H	probably damaging	Het
Rb1	A	T	14: 73,520,363 (GRCm39)	C215*	probably null	Het
Rgs22	A	G	15: 36,015,789 (GRCm39)	S1156P	possibly damaging	Het
Rgs9bp	T	C	7: 35,284,126 (GRCm39)	T174A	probably damaging	Het
Rnf133	A	T	6: 23,649,667 (GRCm39)	Y130*	probably null	Het
Sctr	G	A	1: 119,949,955 (GRCm39)	R48Q	probably benign	Het
Serpinb6e	A	T	13: 34,022,923 (GRCm39)	F153L	probably benign	Het
Slc22a1	A	T	17: 12,885,587 (GRCm39)	Y200N	probably damaging	Het
Slc22a22	C	A	15: 57,113,107 (GRCm39)	M377I	probably benign	Het
Slc36a4	A	G	9: 15,633,452 (GRCm39)		probably null	Het
Slc39a6	A	G	18: 24,734,260 (GRCm39)	V143A	probably benign	Het
Slf2	G	A	19: 44,926,863 (GRCm39)		probably null	Het
Sowaha	T	C	11: 53,370,485 (GRCm39)	K84E	probably benign	Het
Spef2	T	G	15: 9,653,098 (GRCm39)		probably null	Het
Sphkap	A	T	1: 83,254,399 (GRCm39)	F1117I	probably damaging	Het
Tas2r113	T	C	6: 132,870,539 (GRCm39)	I189T	possibly damaging	Het
Tescl	T	C	7: 24,033,247 (GRCm39)	E26G	possibly damaging	Het
Trpm6	A	T	19: 18,854,150 (GRCm39)	I1847F	probably damaging	Het
Uba1y	T	A	Y: 822,200 (GRCm39)	C178S	possibly damaging	Het
Ush2a	T	A	1: 188,175,526 (GRCm39)	V1208D	possibly damaging	Het
Usp13	G	C	3: 32,949,000 (GRCm39)	A446P	probably damaging	Het
Usp7	A	T	16: 8,514,588 (GRCm39)	C722S	possibly damaging	Het
Vmn1r52	A	G	6: 90,156,535 (GRCm39)	S280G	probably benign	Het
Vmn2r84	T	C	10: 130,225,077 (GRCm39)	K478E	probably damaging	Het
Zfp112	C	A	7: 23,824,952 (GRCm39)	L311I	probably benign	Het
Zfp180	G	T	7: 23,805,125 (GRCm39)	E515*	probably null	Het
Zfp518b	A	G	5: 38,829,671 (GRCm39)	I778T	probably damaging	Het
Zfp800	A	T	6: 28,243,662 (GRCm39)	H434Q	probably benign	Het

Other mutations in Cdk5rap1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01778:Cdk5rap1	APN	2	154,207,956 (GRCm39)	missense	probably damaging	1.00
IGL02162:Cdk5rap1	APN	2	154,177,489 (GRCm39)	missense	probably damaging	0.98
IGL02626:Cdk5rap1	APN	2	154,207,880 (GRCm39)	critical splice donor site	probably null
IGL03278:Cdk5rap1	APN	2	154,212,622 (GRCm39)	missense	probably benign	0.00
R1052:Cdk5rap1	UTSW	2	154,202,519 (GRCm39)	missense	possibly damaging	0.96
R1333:Cdk5rap1	UTSW	2	154,202,574 (GRCm39)	missense	probably damaging	0.97
R1552:Cdk5rap1	UTSW	2	154,212,615 (GRCm39)	missense	probably benign	0.00
R1553:Cdk5rap1	UTSW	2	154,194,171 (GRCm39)	missense	probably damaging	1.00
R2107:Cdk5rap1	UTSW	2	154,195,166 (GRCm39)	missense	probably benign	0.22
R3946:Cdk5rap1	UTSW	2	154,190,636 (GRCm39)	missense	probably damaging	1.00
R4126:Cdk5rap1	UTSW	2	154,210,815 (GRCm39)	missense	probably damaging	1.00
R4715:Cdk5rap1	UTSW	2	154,203,755 (GRCm39)	makesense	probably null
R4865:Cdk5rap1	UTSW	2	154,212,876 (GRCm39)	critical splice acceptor site	probably null
R4866:Cdk5rap1	UTSW	2	154,212,876 (GRCm39)	critical splice acceptor site	probably null
R4867:Cdk5rap1	UTSW	2	154,212,876 (GRCm39)	critical splice acceptor site	probably null
R4946:Cdk5rap1	UTSW	2	154,210,794 (GRCm39)	missense	possibly damaging	0.91
R5087:Cdk5rap1	UTSW	2	154,184,315 (GRCm39)	missense	probably damaging	1.00
R5319:Cdk5rap1	UTSW	2	154,177,489 (GRCm39)	missense	possibly damaging	0.62
R5383:Cdk5rap1	UTSW	2	154,192,755 (GRCm39)	missense	possibly damaging	0.78
R5582:Cdk5rap1	UTSW	2	154,187,894 (GRCm39)	missense	probably benign	0.01
R5780:Cdk5rap1	UTSW	2	154,187,788 (GRCm39)	frame shift	probably null
R6262:Cdk5rap1	UTSW	2	154,212,606 (GRCm39)	missense	probably benign	0.04
R6274:Cdk5rap1	UTSW	2	154,210,161 (GRCm39)	missense	probably damaging	0.99
R7388:Cdk5rap1	UTSW	2	154,202,595 (GRCm39)	missense	probably damaging	1.00
R7650:Cdk5rap1	UTSW	2	154,196,036 (GRCm39)	missense	probably benign	0.01
R8424:Cdk5rap1	UTSW	2	154,187,932 (GRCm39)	missense	probably damaging	1.00
R8694:Cdk5rap1	UTSW	2	154,195,148 (GRCm39)	nonsense	probably null
R9295:Cdk5rap1	UTSW	2	154,194,186 (GRCm39)	missense	probably damaging	1.00
R9413:Cdk5rap1	UTSW	2	154,207,880 (GRCm39)	critical splice donor site	probably null
R9453:Cdk5rap1	UTSW	2	154,190,585 (GRCm39)	missense	probably damaging	1.00
R9466:Cdk5rap1	UTSW	2	154,192,756 (GRCm39)	missense	possibly damaging	0.64

Predicted Primers

PCR Primer
(F):5'- GCAAGCATATACTATCGCAGC -3'
(R):5'- TTGAAAATAGGGGTTCAGTGCAATG -3'

Sequencing Primer
(F):5'- GCTACTTAGAGAAACCCTGTCTGG -3'
(R):5'- AATGGGTTTGGTTTGAAGGATAATAG -3'

Posted On

2019-06-26