Mutagenetix > Incidental Mutation

Incidental Mutation 'R3946:Cdk5rap1'

307693

Institutional Source

Beutler Lab

Gene Symbol

Cdk5rap1

Ensembl Gene

ENSMUSG00000027487

Gene Name

CDK5 regulatory subunit associated protein 1

Synonyms

2310066P17Rik

MMRRC Submission

040827-MU

Accession Numbers

Essential gene?

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

Stock #

R3946 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

154177300-154214930 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 154190636 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 442 (T442A)

Ref Sequence

ENSEMBL: ENSMUSP00000105353 (fasta)

Gene Model

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

AlphaFold

Q8BTW8

Predicted Effect

probably damaging
Transcript: ENSMUST00000028990
AA Change: T442A

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

SMART Domains

Protein: ENSMUSP00000028990
Gene: ENSMUSG00000027487
AA Change: T442A

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 damaging
Transcript: ENSMUST00000109731
AA Change: T442A

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

SMART Domains

Protein: ENSMUSP00000105353
Gene: ENSMUSG00000027487
AA Change: T442A

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148289

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152180

Meta Mutation Damage Score

0.9497

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.0%
20x: 94.1%

Validation Efficiency

98% (60/61)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abi2	A	G	1: 60,492,913 (GRCm39)	Q328R	probably damaging	Het
Agr3	C	A	12: 35,997,512 (GRCm39)		probably benign	Het
Brca2	T	A	5: 150,460,169 (GRCm39)	S481R	probably damaging	Het
Cabin1	T	G	10: 75,581,093 (GRCm39)	Q411P	probably damaging	Het
Calr3	A	G	8: 73,197,464 (GRCm39)	Y22H	probably damaging	Het
Caprin1	T	A	2: 103,627,111 (GRCm39)	I59F	probably damaging	Het
Chn2	T	C	6: 54,246,411 (GRCm39)		probably benign	Het
Cic	C	A	7: 24,971,771 (GRCm39)	R501S	possibly damaging	Het
Coch	A	G	12: 51,648,595 (GRCm39)		probably null	Het
Defa25	G	A	8: 21,574,506 (GRCm39)	V17I	probably null	Het
Dglucy	T	C	12: 100,804,959 (GRCm39)		probably null	Het
Dtx1	T	G	5: 120,819,351 (GRCm39)	T616P	possibly damaging	Het
Eef1g	T	C	19: 8,947,341 (GRCm39)	L171P	probably benign	Het
Fam135a	A	G	1: 24,069,475 (GRCm39)	S465P	probably damaging	Het
Gm14412	A	T	2: 177,006,478 (GRCm39)	C472*	probably null	Het
Gm7104	T	C	12: 88,252,812 (GRCm39)		noncoding transcript	Het
Got2	A	G	8: 96,614,858 (GRCm39)	S26P	probably benign	Het
H2-M11	A	G	17: 36,860,123 (GRCm39)	I329M	probably damaging	Het
Hmcn2	T	A	2: 31,272,406 (GRCm39)	D1295E	possibly damaging	Het
Hoxd12	G	T	2: 74,505,771 (GRCm39)	R114L	probably damaging	Het
Ilkap	A	C	1: 91,314,972 (GRCm39)	D124E	probably damaging	Het
Maco1	A	G	4: 134,531,792 (GRCm39)	Y626H	probably damaging	Het
Med6	T	C	12: 81,628,625 (GRCm39)	Y88C	probably damaging	Het
Mep1a	A	T	17: 43,785,932 (GRCm39)	L719*	probably null	Het
Mmp23	T	C	4: 155,736,480 (GRCm39)	Y187C	probably damaging	Het
Myo1g	A	G	11: 6,470,760 (GRCm39)	M32T	possibly damaging	Het
Ncstn	T	C	1: 171,895,061 (GRCm39)	E614G	probably benign	Het
Nr2c2	C	T	6: 92,140,119 (GRCm39)	R464W	probably damaging	Het
Or4f15	G	A	2: 111,813,642 (GRCm39)	T259M	possibly damaging	Het
Otub2	T	A	12: 103,359,085 (GRCm39)	L58*	probably null	Het
Pcdhga12	G	A	18: 37,900,682 (GRCm39)	V505I	probably benign	Het
Pcdhga9	T	A	18: 37,870,897 (GRCm39)	V242D	probably damaging	Het
Pex1	C	T	5: 3,676,084 (GRCm39)	L891F	probably damaging	Het
Pgm2	C	T	5: 64,269,404 (GRCm39)	T497I	probably benign	Het
Pikfyve	T	C	1: 65,235,840 (GRCm39)	F171L	probably damaging	Het
Pilrb1	T	G	5: 137,855,654 (GRCm39)	K79T	probably benign	Het
Pin1	C	T	9: 20,566,660 (GRCm39)	R21W	probably damaging	Het
Prxl2c	T	C	13: 64,456,912 (GRCm39)	I104V	probably damaging	Het
Ptprq	A	G	10: 107,522,253 (GRCm39)		probably benign	Het
Rad17	G	A	13: 100,759,371 (GRCm39)	A552V	possibly damaging	Het
Rbbp8	A	G	18: 11,851,925 (GRCm39)	T249A	probably benign	Het
Rtkn	A	T	6: 83,112,957 (GRCm39)	I10F	probably benign	Het
Scube2	T	A	7: 109,456,797 (GRCm39)	I103F	possibly damaging	Het
Sec23b	A	G	2: 144,423,893 (GRCm39)	H514R	probably benign	Het
Serbp1	T	A	6: 67,249,204 (GRCm39)	D223E	probably benign	Het
Slc14a1	C	A	18: 78,154,607 (GRCm39)	V260L	probably benign	Het
Slc22a23	A	G	13: 34,367,109 (GRCm39)	I633T	probably damaging	Het
Stk19	A	T	17: 35,043,723 (GRCm39)		probably benign	Het
Svs5	T	C	2: 164,079,047 (GRCm39)	M287V	probably benign	Het
Syne3	T	A	12: 104,924,325 (GRCm39)	Q358L	probably damaging	Het
Synj1	A	G	16: 90,806,984 (GRCm39)	F58L	possibly damaging	Het
Tg	T	C	15: 66,545,872 (GRCm39)	V198A	probably damaging	Het
Tle4	A	T	19: 14,574,752 (GRCm39)	Y9N	probably damaging	Het
Tmx3	G	A	18: 90,542,459 (GRCm39)	A186T	possibly damaging	Het
Traf3	G	A	12: 111,221,679 (GRCm39)	S280N	possibly damaging	Het
Trmt13	A	G	3: 116,375,167 (GRCm39)	F447S	probably damaging	Het
Trp53bp1	T	A	2: 121,059,107 (GRCm39)	H918L	probably damaging	Het
Ush2a	T	G	1: 188,460,701 (GRCm39)	V2654G	probably benign	Het
Vinac1	A	G	2: 128,881,521 (GRCm39)	L135P	probably damaging	Het
Vmn2r25	A	G	6: 123,817,057 (GRCm39)	Y175H	probably damaging	Het
Zfp335	T	C	2: 164,734,109 (GRCm39)	D1330G	probably damaging	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
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
R7263:Cdk5rap1	UTSW	2	154,202,652 (GRCm39)	missense	probably benign	0.12
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'- GGGACTTTACCAGGTCTGTCTTC -3'
(R):5'- TCCCCTTGCTCTGTAAGGAC -3'

Sequencing Primer
(F):5'- AGGTCTGTCTTCTTGTCACAC -3'
(R):5'- TTAAAGGGATGTGCTACCATGCCC -3'

Posted On

2015-04-17