Mutagenetix > Incidental Mutation

Incidental Mutation 'R8117:Cdkn2d'

631278

Institutional Source

Beutler Lab

Gene Symbol

Cdkn2d

Ensembl Gene

ENSMUSG00000096472

Gene Name

cyclin dependent kinase inhibitor 2D

Synonyms

INK4d, p19, p19INK4d, INK4d

MMRRC Submission

067546-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.260) question?

Stock #

R8117 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

21199759-21202553 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 21200447 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Leucine at position 108 (S108L)

Ref Sequence

ENSEMBL: ENSMUSP00000150701 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038671] [ENSMUST00000086374] [ENSMUST00000184326] [ENSMUST00000213407] [ENSMUST00000215619]

AlphaFold

Q60773

Predicted Effect

probably benign
Transcript: ENSMUST00000038671

SMART Domains

Protein: ENSMUSP00000039688
Gene: ENSMUSG00000035047

Domain	Start	End	E-Value	Type
low complexity region	20	34	N/A	INTRINSIC
low complexity region	50	60	N/A	INTRINSIC
low complexity region	98	112	N/A	INTRINSIC
low complexity region	181	195	N/A	INTRINSIC
Pfam:Kri1	346	439	3.2e-27	PFAM
Pfam:Kri1_C	507	595	8.4e-37	PFAM
low complexity region	653	666	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000086374

SMART Domains

Protein: ENSMUSP00000083561
Gene: ENSMUSG00000096472

Domain	Start	End	E-Value	Type
ANK	41	69	1.01e2	SMART
ANK	73	102	1.73e-4	SMART
ANK	106	134	8.89e1	SMART
Blast:ANK	138	166	1e-9	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000184326

SMART Domains

Protein: ENSMUSP00000139184
Gene: ENSMUSG00000035047

Domain	Start	End	E-Value	Type
low complexity region	57	71	N/A	INTRINSIC
Pfam:Kri1	207	317	4.4e-27	PFAM
Pfam:Kri1_C	381	472	3.6e-36	PFAM
low complexity region	529	542	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000213407
AA Change: S108L

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

Predicted Effect

probably benign
Transcript: ENSMUST00000215619
AA Change: S108L

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

Coding Region Coverage

1x: 99.8%
3x: 99.5%
10x: 98.5%
20x: 94.4%

Validation Efficiency

99% (73/74)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the INK4 family of cyclin-dependent kinase inhibitors. This protein has been shown to form a stable complex with CDK4 or CDK6, and prevent the activation of the CDK kinases, thus function as a cell growth regulator that controls cell cycle G1 progression. The abundance of the transcript of this gene was found to oscillate in a cell-cycle dependent manner with the lowest expression at mid G1 and a maximal expression during S phase. The negative regulation of the cell cycle involved in this protein was shown to participate in repressing neuronal proliferation, as well as spermatogenesis. Two alternatively spliced variants of this gene, which encode an identical protein, have been reported. [provided by RefSeq, Jul 2008]
PHENOTYPE: Both female and male homozygous null mice are fertile in spite of testicular atrophy and increased male germ cell apoptosis due to delayed meiosis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010315B03Rik	T	C	9: 124,058,078 (GRCm39)	T14A		Het
2610008E11Rik	T	C	10: 78,930,289 (GRCm39)	N42D	probably benign	Het
Ajm1	A	G	2: 25,469,246 (GRCm39)	F222L	probably benign	Het
Ankrd54	T	A	15: 78,939,641 (GRCm39)	M183L		Het
Apob	G	A	12: 8,056,435 (GRCm39)	G1639D	probably damaging	Het
B3gat2	A	G	1: 23,884,061 (GRCm39)	T283A	probably benign	Het
Bmpr2	T	G	1: 59,886,252 (GRCm39)	S296R	probably damaging	Het
Cand1	G	A	10: 119,042,721 (GRCm39)	T1123I	probably damaging	Het
Cc2d2a	T	C	5: 43,869,781 (GRCm39)	F943S	probably damaging	Het
Ccdc40	T	C	11: 119,144,211 (GRCm39)	I912T	probably benign	Het
Cep295	G	A	9: 15,245,660 (GRCm39)	T932I	probably damaging	Het
Cntn5	A	G	9: 9,673,955 (GRCm39)	S716P	probably benign	Het
Col18a1	T	C	10: 76,895,808 (GRCm39)	E903G	probably benign	Het
Ctrc	T	A	4: 141,565,972 (GRCm39)	I229F	probably damaging	Het
Cyb561d2	C	T	9: 107,418,771 (GRCm39)	A18T	probably benign	Het
Dnajb4	T	A	3: 151,899,089 (GRCm39)	K46*	probably null	Het
Dsc2	C	T	18: 20,165,331 (GRCm39)	G881R	possibly damaging	Het
Dsg1c	C	T	18: 20,410,016 (GRCm39)	H495Y	probably benign	Het
Eif2b3	A	G	4: 116,879,414 (GRCm39)	D18G	probably damaging	Het
Enam	A	T	5: 88,651,385 (GRCm39)	I965L	probably benign	Het
Fhod3	T	A	18: 25,248,910 (GRCm39)	I1363K	probably damaging	Het
Fras1	A	G	5: 96,855,245 (GRCm39)	Y1918C	probably damaging	Het
Fsip2	T	A	2: 82,823,296 (GRCm39)	I6343N	possibly damaging	Het
Gpr45	G	C	1: 43,072,475 (GRCm39)	V373L	probably damaging	Het
Hdac2	G	T	10: 36,873,966 (GRCm39)	Q365H	probably damaging	Het
Hspa12b	A	G	2: 130,980,389 (GRCm39)	T103A	possibly damaging	Het
Ifrd1	A	T	12: 40,262,350 (GRCm39)	S287T	probably benign	Het
Igkv6-15	G	A	6: 70,383,622 (GRCm39)	P60S	possibly damaging	Het
Ippk	C	T	13: 49,599,818 (GRCm39)	P226S		Het
Kctd19	T	A	8: 106,122,069 (GRCm39)	D109V	unknown	Het
Matn4	G	A	2: 164,234,851 (GRCm39)	S540L	probably damaging	Het
Matn4	T	C	2: 164,241,682 (GRCm39)	K248E	probably benign	Het
Muc16	G	A	9: 18,420,206 (GRCm39)	Q97*	probably null	Het
Mup18	A	G	4: 61,592,238 (GRCm39)	C9R	unknown	Het
Myh1	A	G	11: 67,113,031 (GRCm39)	K1845R	probably damaging	Het
Mysm1	G	A	4: 94,848,627 (GRCm39)	R469*	probably null	Het
Naip1	T	C	13: 100,563,509 (GRCm39)	D552G	possibly damaging	Het
Nrcam	A	G	12: 44,618,371 (GRCm39)	D787G	probably benign	Het
Nrcam	G	A	12: 44,645,365 (GRCm39)	V1256I	probably damaging	Het
Obscn	G	T	11: 58,932,980 (GRCm39)	H4799N	possibly damaging	Het
Or1f12	T	C	13: 21,722,122 (GRCm39)	K3E	probably benign	Het
Or4p4	A	G	2: 88,482,729 (GRCm39)	K78E	probably damaging	Het
Or52e18	T	C	7: 104,609,356 (GRCm39)	I194M	probably damaging	Het
Or7g22	A	G	9: 19,048,353 (GRCm39)	I21M	probably benign	Het
Pcdhgb5	T	C	18: 37,866,302 (GRCm39)	F699S	probably damaging	Het
Phtf2	T	C	5: 21,007,038 (GRCm39)	E175G	probably benign	Het
Pira1	G	A	7: 3,740,075 (GRCm39)	T340I	probably damaging	Het
Ppp2r5c	A	G	12: 110,517,519 (GRCm39)	H218R	possibly damaging	Het
Ptgs2	A	G	1: 149,979,785 (GRCm39)	R297G	probably damaging	Het
Rapgef3	A	T	15: 97,648,747 (GRCm39)	D619E	probably benign	Het
Ric1	G	A	19: 29,552,191 (GRCm39)	V321I	probably benign	Het
Ripor1	T	C	8: 106,344,105 (GRCm39)	V413A	probably damaging	Het
Rsf1	G	T	7: 97,288,464 (GRCm39)		probably null	Het
Sccpdh	A	G	1: 179,504,017 (GRCm39)	D122G	probably damaging	Het
Sec16a	A	T	2: 26,331,441 (GRCm39)	H191Q	probably benign	Het
Slco1a5	G	T	6: 142,208,418 (GRCm39)	N124K	probably damaging	Het
Snrnp200	A	G	2: 127,071,051 (GRCm39)	T1111A	probably benign	Het
Stard9	G	A	2: 120,534,911 (GRCm39)	G3723S	probably benign	Het
Tanc2	T	A	11: 105,725,988 (GRCm39)	V384E	probably damaging	Het
Tbrg1	A	G	9: 37,568,296 (GRCm39)	F49L	possibly damaging	Het
Tecta	A	G	9: 42,288,927 (GRCm39)	F546S	probably damaging	Het
Tmem132c	A	G	5: 127,437,176 (GRCm39)	R222G	probably benign	Het
Trub2	C	T	2: 29,668,739 (GRCm39)		probably null	Het
Tti1	G	T	2: 157,849,418 (GRCm39)	P607Q	probably damaging	Het
Vmn1r62	T	A	7: 5,678,726 (GRCm39)	F136I	possibly damaging	Het
Vmn2r111	T	A	17: 22,790,469 (GRCm39)	H179L	probably benign	Het
Wdfy4	A	T	14: 32,699,063 (GRCm39)	C2703*	probably null	Het
Wdfy4	G	A	14: 32,826,072 (GRCm39)	P1193L		Het
Wipf3	A	G	6: 54,460,816 (GRCm39)	K88R	probably benign	Het
Zfp641	C	T	15: 98,186,856 (GRCm39)	G256R	probably damaging	Het
Zfp993	T	A	4: 146,741,972 (GRCm39)	C99S	probably benign	Het

Other mutations in Cdkn2d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02516:Cdkn2d	APN	9	21,200,439 (GRCm39)	missense	probably benign	0.04
R0238:Cdkn2d	UTSW	9	21,202,288 (GRCm39)	start gained	probably benign
R0238:Cdkn2d	UTSW	9	21,202,288 (GRCm39)	start gained	probably benign
R2064:Cdkn2d	UTSW	9	21,202,175 (GRCm39)	missense	probably damaging	1.00
R4454:Cdkn2d	UTSW	9	21,202,185 (GRCm39)	missense	probably benign
R4455:Cdkn2d	UTSW	9	21,202,185 (GRCm39)	missense	probably benign
R4456:Cdkn2d	UTSW	9	21,202,185 (GRCm39)	missense	probably benign
R4457:Cdkn2d	UTSW	9	21,202,185 (GRCm39)	missense	probably benign
R4458:Cdkn2d	UTSW	9	21,202,185 (GRCm39)	missense	probably benign
R4462:Cdkn2d	UTSW	9	21,202,185 (GRCm39)	missense	probably benign
R4463:Cdkn2d	UTSW	9	21,202,185 (GRCm39)	missense	probably benign
R4735:Cdkn2d	UTSW	9	21,202,185 (GRCm39)	missense	probably benign
R4854:Cdkn2d	UTSW	9	21,202,223 (GRCm39)	missense	probably benign
R5493:Cdkn2d	UTSW	9	21,200,303 (GRCm39)	missense	probably benign	0.00
R7560:Cdkn2d	UTSW	9	21,200,540 (GRCm39)	missense	probably damaging	1.00
R9603:Cdkn2d	UTSW	9	21,202,139 (GRCm39)	missense	possibly damaging	0.91
R9762:Cdkn2d	UTSW	9	21,200,383 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- ATTGGGATCATCATGTGCCCC -3'
(R):5'- GACCCTTCTCCAATGGGAAC -3'

Sequencing Primer
(F):5'- CCTGCAGAATGTCCATGAGGTTC -3'
(R):5'- ACCCCCATAGGTCATGATGTTTGG -3'

Posted On

2020-06-30