Mutagenetix > Incidental Mutation

Incidental Mutation 'R5214:Ndrg1'

403373

Institutional Source

Beutler Lab

Gene Symbol

Ndrg1

Ensembl Gene

ENSMUSG00000005125

Gene Name

N-myc downstream regulated gene 1

Synonyms

DRG1, Ndrl, PROXY1, Tdd5, Ndr1, CMT4D, TDD5, CAP43

MMRRC Submission

042787-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5214 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

66801167-66841489 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 66831239 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 24 (T24I)

Ref Sequence

ENSEMBL: ENSMUSP00000130150 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000005256] [ENSMUST00000163496] [ENSMUST00000164070] [ENSMUST00000164675] [ENSMUST00000166420] [ENSMUST00000168542] [ENSMUST00000168979] [ENSMUST00000170903] [ENSMUST00000171266] [ENSMUST00000172447]

AlphaFold

Q62433

Predicted Effect

probably benign
Transcript: ENSMUST00000005256
AA Change: T24I

PolyPhen 2 Score 0.034 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000005256
Gene: ENSMUSG00000005125
AA Change: T24I

Domain	Start	End	E-Value	Type
Pfam:Ndr	34	316	4.4e-130	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000163496
AA Change: T24I

PolyPhen 2 Score 0.095 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000130584
Gene: ENSMUSG00000005125
AA Change: T24I

Domain	Start	End	E-Value	Type
Pfam:Ndr	34	155	1.2e-61	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000164070
AA Change: T24I

PolyPhen 2 Score 0.464 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000126091
Gene: ENSMUSG00000005125
AA Change: T24I

Domain	Start	End	E-Value	Type
Pfam:Ndr	18	53	8.5e-10	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000164675
AA Change: T24I

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

Predicted Effect

probably benign
Transcript: ENSMUST00000166420
AA Change: T24I

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000127099
Gene: ENSMUSG00000005125
AA Change: T24I

Domain	Start	End	E-Value	Type
Pfam:Ndr	17	132	1.4e-34	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000168542
AA Change: T24I

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)

Predicted Effect

probably benign
Transcript: ENSMUST00000168979
AA Change: T24I

PolyPhen 2 Score 0.059 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000126985
Gene: ENSMUSG00000005125
AA Change: T24I

Domain	Start	End	E-Value	Type
Pfam:Ndr	34	174	6.3e-72	PFAM
Pfam:Abhydrolase_6	53	173	5.3e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000170903
AA Change: T24I

PolyPhen 2 Score 0.154 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000127302
Gene: ENSMUSG00000005125
AA Change: T24I

Domain	Start	End	E-Value	Type
Pfam:Ndr	34	157	1.2e-62	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000171266
AA Change: T24I

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)

Predicted Effect

probably damaging
Transcript: ENSMUST00000172447
AA Change: T24I

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000171569

Meta Mutation Damage Score

0.1864

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.9%

Validation Efficiency

100% (77/77)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the N-myc downregulated gene family which belongs to the alpha/beta hydrolase superfamily. The protein encoded by this gene is a cytoplasmic protein involved in stress responses, hormone responses, cell growth, and differentiation. The encoded protein is necessary for p53-mediated caspase activation and apoptosis. Mutations in this gene are a cause of Charcot-Marie-Tooth disease type 4D, and expression of this gene may be a prognostic indicator for several types of cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]
PHENOTYPE: Homozygous null mice exhibit a progressive demyelinating disorder of the peripheral nerves with hindlimb weakness. Mice homozygous for a different knock-out allele exhibit decreased cellular susceptibility to gamma-irradiation and increased susceptibility to spontaneous and induced tumors. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700061I17Rik	A	G	3: 116,861,424 (GRCm39)		noncoding transcript	Het
4930449A18Rik	A	T	3: 59,733,305 (GRCm39)		noncoding transcript	Het
Acsbg3	T	C	17: 57,193,493 (GRCm39)	V613A	probably benign	Het
Adgrl1	G	A	8: 84,642,202 (GRCm39)		probably null	Het
Aldh1l1	A	G	6: 90,540,399 (GRCm39)	D228G	probably damaging	Het
Ankrd17	T	C	5: 90,431,319 (GRCm39)	I822V	possibly damaging	Het
Atm	C	A	9: 53,402,327 (GRCm39)	A1382S	probably benign	Het
Bltp3a	G	A	17: 28,106,489 (GRCm39)	S1005N	probably benign	Het
Cacna1e	T	A	1: 154,577,110 (GRCm39)	I96F	possibly damaging	Het
Calhm5	A	G	10: 33,968,487 (GRCm39)	S189P	probably damaging	Het
Ccar1	G	A	10: 62,606,740 (GRCm39)	R335C	probably damaging	Het
Ccdc113	T	C	8: 96,272,601 (GRCm39)	I236T	possibly damaging	Het
Ccdc14	T	A	16: 34,525,225 (GRCm39)	S125T	probably benign	Het
Cdc45	C	T	16: 18,614,647 (GRCm39)	R205H	probably damaging	Het
Cdon	T	C	9: 35,394,504 (GRCm39)	C917R	probably damaging	Het
Ckap2l	T	C	2: 129,127,389 (GRCm39)	D263G	probably benign	Het
Cntnap3	G	T	13: 64,909,824 (GRCm39)	H760Q	probably damaging	Het
Dennd2d	G	A	3: 106,393,637 (GRCm39)		probably null	Het
Dock4	A	G	12: 40,754,465 (GRCm39)	I485V	probably benign	Het
Dspp	A	G	5: 104,326,364 (GRCm39)	D909G	unknown	Het
Eps8	A	T	6: 137,504,490 (GRCm39)	M81K	probably damaging	Het
Fras1	T	C	5: 96,917,452 (GRCm39)	S3491P	probably damaging	Het
Gm17669	C	T	18: 67,695,479 (GRCm39)	T8I	possibly damaging	Het
Gm5114	G	T	7: 39,057,792 (GRCm39)	T609K	probably benign	Het
Gm973	A	G	1: 59,565,880 (GRCm39)	N32S	probably damaging	Het
Herpud1	G	T	8: 95,117,479 (GRCm39)		probably null	Het
Jcad	T	A	18: 4,674,134 (GRCm39)	L632Q	probably damaging	Het
Kcnh8	T	C	17: 53,205,486 (GRCm39)	L527S	probably damaging	Het
Klk1b11	C	A	7: 43,647,266 (GRCm39)	H67N	probably benign	Het
Ldhb	T	A	6: 142,441,321 (GRCm39)	I190F	probably damaging	Het
Lrrc34	A	T	3: 30,690,397 (GRCm39)	C168*	probably null	Het
Lrtm1	C	T	14: 28,743,651 (GRCm39)	H40Y	possibly damaging	Het
Mageb3	T	C	2: 121,785,319 (GRCm39)	M128V	possibly damaging	Het
Miga2	A	G	2: 30,261,208 (GRCm39)	T90A	probably benign	Het
Msantd5	C	A	11: 51,125,675 (GRCm39)	H199Q	possibly damaging	Het
Nos2	T	C	11: 78,846,267 (GRCm39)	L878P	probably damaging	Het
Or11g27	T	G	14: 50,771,804 (GRCm39)	*312E	probably null	Het
Pcdhgb1	T	A	18: 37,814,478 (GRCm39)	I323N	probably damaging	Het
Plec	A	G	15: 76,061,921 (GRCm39)	I2537T	probably damaging	Het
Pnpo	C	A	11: 96,833,295 (GRCm39)	E68D	probably benign	Het
Ppp6r1	C	T	7: 4,646,176 (GRCm39)	R175Q	probably benign	Het
Prnp	C	T	2: 131,778,924 (GRCm39)	T192I	probably damaging	Het
Ptprb	T	C	10: 116,205,229 (GRCm39)	I2148T	possibly damaging	Het
Raf1	G	T	6: 115,614,583 (GRCm39)	F99L	possibly damaging	Het
Rbks	A	G	5: 31,807,736 (GRCm39)		probably benign	Het
Rlf	T	C	4: 121,007,897 (GRCm39)	D361G	probably damaging	Het
Rnpepl1	G	T	1: 92,847,001 (GRCm39)	D608Y	probably benign	Het
Scaf1	G	A	7: 44,652,662 (GRCm39)		probably benign	Het
Sh3rf1	A	T	8: 61,825,765 (GRCm39)	M587L	probably damaging	Het
Slc22a21	A	T	11: 53,843,869 (GRCm39)	S473T	probably damaging	Het
Syt15	A	G	14: 33,943,703 (GRCm39)	D84G	possibly damaging	Het
Tbc1d19	T	C	5: 54,007,183 (GRCm39)	L236P	probably benign	Het
Tbx2	G	T	11: 85,729,263 (GRCm39)	A549S	probably benign	Het
Tc2n	A	T	12: 101,659,461 (GRCm39)	C157*	probably null	Het
Tecta	C	T	9: 42,256,964 (GRCm39)	V1571I	probably benign	Het
Them4	A	G	3: 94,224,818 (GRCm39)	K65R	probably benign	Het
Tmc5	C	T	7: 118,247,155 (GRCm39)	T553M	probably damaging	Het
Tmem200c	C	T	17: 69,148,122 (GRCm39)	A235V	probably damaging	Het
Tmem8b	G	A	4: 43,673,992 (GRCm39)	V208I	probably benign	Het
Tmf1	G	C	6: 97,144,253 (GRCm39)	A701G	possibly damaging	Het
Tomm70a	G	A	16: 56,942,300 (GRCm39)	G26S	unknown	Het
Treh	T	C	9: 44,594,173 (GRCm39)	Y140H	probably damaging	Het
Ttc28	A	G	5: 111,325,489 (GRCm39)		probably benign	Het
Uba7	T	C	9: 107,854,713 (GRCm39)		probably benign	Het
Ube4a	T	C	9: 44,860,166 (GRCm39)	I299V	probably benign	Het
Zfhx4	A	C	3: 5,468,701 (GRCm39)	K2953T	probably damaging	Het
Zfp280d	T	A	9: 72,215,395 (GRCm39)		probably benign	Het
Zscan20	G	A	4: 128,482,109 (GRCm39)	R518C	probably benign	Het
Zw10	T	C	9: 48,975,463 (GRCm39)	I296T	possibly damaging	Het

Other mutations in Ndrg1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00923:Ndrg1	APN	15	66,814,959 (GRCm39)	missense	probably damaging	1.00
IGL01419:Ndrg1	APN	15	66,802,900 (GRCm39)	missense	probably benign	0.01
IGL02618:Ndrg1	APN	15	66,812,086 (GRCm39)	missense	probably benign	0.03
IGL02869:Ndrg1	APN	15	66,818,346 (GRCm39)	missense	probably benign	0.01
IGL03206:Ndrg1	APN	15	66,814,936 (GRCm39)	nonsense	probably null
PIT4377001:Ndrg1	UTSW	15	66,820,288 (GRCm39)	missense	probably benign
R0328:Ndrg1	UTSW	15	66,815,008 (GRCm39)	splice site	probably benign
R1102:Ndrg1	UTSW	15	66,816,685 (GRCm39)	missense	probably damaging	1.00
R1105:Ndrg1	UTSW	15	66,812,080 (GRCm39)	missense	probably damaging	0.99
R1748:Ndrg1	UTSW	15	66,802,930 (GRCm39)	missense	possibly damaging	0.55
R1875:Ndrg1	UTSW	15	66,802,940 (GRCm39)	missense	possibly damaging	0.91
R5809:Ndrg1	UTSW	15	66,802,699 (GRCm39)	unclassified	probably benign
R6433:Ndrg1	UTSW	15	66,805,721 (GRCm39)	missense	probably damaging	1.00
R7104:Ndrg1	UTSW	15	66,818,377 (GRCm39)	missense	probably damaging	1.00
R7412:Ndrg1	UTSW	15	66,832,382 (GRCm39)	start codon destroyed	probably null	1.00
R7424:Ndrg1	UTSW	15	66,816,787 (GRCm39)	splice site	probably null
R7667:Ndrg1	UTSW	15	66,820,243 (GRCm39)	missense	probably damaging	1.00
R9220:Ndrg1	UTSW	15	66,805,711 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- CGGGTAGAACTCAAACTAGCTTC -3'
(R):5'- CCAATTTTCTACTGGGCTGCTG -3'

Sequencing Primer
(F):5'- TCAAACTAGCTTCTTCCAGGAG -3'
(R):5'- GGCTGCTGTTCCCTGAGATAAAAC -3'

Posted On

2016-07-22