Mutagenetix > Incidental Mutation

Incidental Mutation 'R4728:Npdc1'

358578

Institutional Source

Beutler Lab

Gene Symbol

Npdc1

Ensembl Gene

ENSMUSG00000015094

Gene Name

neural proliferation, differentiation and control 1

Synonyms

NPDC-1

MMRRC Submission

042020-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4728 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

25293062-25299506 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 25298957 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Asparagine at position 284 (D284N)

Ref Sequence

ENSEMBL: ENSMUSP00000071387 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000055921] [ENSMUST00000071442] [ENSMUST00000133409] [ENSMUST00000141567] [ENSMUST00000154809]

AlphaFold

Q64322

Predicted Effect

probably damaging
Transcript: ENSMUST00000055921
AA Change: D293N

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000049602
Gene: ENSMUSG00000015094
AA Change: D293N

Domain	Start	End	E-Value	Type
Pfam:NPDC1	1	341	9.1e-234	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000071442
AA Change: D284N

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

SMART Domains

Protein: ENSMUSP00000071387
Gene: ENSMUSG00000015094
AA Change: D284N

Domain	Start	End	E-Value	Type
Pfam:NPDC1	1	332	7.2e-217	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124277

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128144

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131185

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132287

Predicted Effect

possibly damaging
Transcript: ENSMUST00000133409
AA Change: D226N

PolyPhen 2 Score 0.953 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000117773
Gene: ENSMUSG00000015094
AA Change: D226N

Domain	Start	End	E-Value	Type
Pfam:NPDC1	1	274	3.4e-163	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138651

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136138

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144413

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141106

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156824

Predicted Effect

probably benign
Transcript: ENSMUST00000141567

SMART Domains

Protein: ENSMUSP00000116275
Gene: ENSMUSG00000015094

Domain	Start	End	E-Value	Type
Pfam:NPDC1	1	231	7.8e-141	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000154809

SMART Domains

Protein: ENSMUSP00000123386
Gene: ENSMUSG00000015094

Domain	Start	End	E-Value	Type
Pfam:NPDC1	1	142	1.8e-88	PFAM

Meta Mutation Damage Score

0.5505

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.3%

Validation Efficiency

94% (73/78)

MGI Phenotype

PHENOTYPE: Homozygous null mice display no obvious abnormalities in viability, fertility, behavior, or brain morphology. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Bicc1	C	T	10: 70,771,661 (GRCm39)		probably null	Het
Bpifc	T	A	10: 85,827,063 (GRCm39)	H162L	possibly damaging	Het
Ccdc163	C	T	4: 116,566,209 (GRCm39)		probably benign	Het
Cldn12	A	G	5: 5,558,385 (GRCm39)	F14S	probably damaging	Het
Cyth4	G	A	15: 78,486,913 (GRCm39)	G14R	probably benign	Het
Ddhd2	C	T	8: 26,242,294 (GRCm39)	V194I	probably damaging	Het
Ddx23	A	T	15: 98,548,106 (GRCm39)	V433E	probably damaging	Het
Defb34	A	G	8: 19,176,434 (GRCm39)	N42D	possibly damaging	Het
Dennd6a	A	G	14: 26,348,575 (GRCm39)	E313G	probably null	Het
Dhx30	A	G	9: 109,916,718 (GRCm39)	F570S	probably damaging	Het
Dnah3	T	C	7: 119,658,589 (GRCm39)	E864G	probably damaging	Het
Eps8	G	A	6: 137,486,160 (GRCm39)	Q451*	probably null	Het
Fmo9	A	T	1: 166,490,880 (GRCm39)	Y533N	possibly damaging	Het
Fut8	T	A	12: 77,521,973 (GRCm39)	D537E	probably damaging	Het
Gm5407	T	C	16: 49,117,283 (GRCm39)		noncoding transcript	Het
Gm9916	A	G	3: 118,228,690 (GRCm39)		noncoding transcript	Het
Grm5	T	A	7: 87,624,496 (GRCm39)	F354L	probably damaging	Het
Hira	C	T	16: 18,741,654 (GRCm39)	A353V	probably damaging	Het
Ifna4	C	A	4: 88,760,519 (GRCm39)	T141K	probably benign	Het
Igf1r	T	C	7: 67,839,372 (GRCm39)	L628P	probably damaging	Het
Kcnh5	A	T	12: 75,054,555 (GRCm39)	I463N	probably damaging	Het
Kcnh8	C	A	17: 53,032,898 (GRCm39)	Q62K	probably damaging	Het
Kif3c	A	T	12: 3,415,873 (GRCm39)		probably benign	Het
Kmo	A	G	1: 175,484,329 (GRCm39)	D353G	possibly damaging	Het
Lrp1	T	C	10: 127,399,606 (GRCm39)	T2301A	probably damaging	Het
Lrrc7	GAAGTTGTTTGGAGATTCTTATCTTA	GA	3: 158,024,045 (GRCm39)		probably benign	Het
Map3k9	C	T	12: 81,769,147 (GRCm39)	R967Q	probably damaging	Het
Mcm8	A	G	2: 132,674,774 (GRCm39)	H414R	probably damaging	Het
Mier1	A	G	4: 102,997,402 (GRCm39)	E145G	probably damaging	Het
Mlc1	A	T	15: 88,862,234 (GRCm39)		probably null	Het
Napb	T	C	2: 148,551,245 (GRCm39)	D96G	probably damaging	Het
Nbas	T	A	12: 13,338,740 (GRCm39)	S193R	probably damaging	Het
Nlrp4a	T	C	7: 26,174,515 (GRCm39)	V967A	probably benign	Het
Nlrp4e	T	A	7: 23,020,989 (GRCm39)	I492K	probably benign	Het
Notch4	A	G	17: 34,789,179 (GRCm39)	T497A	probably benign	Het
Ogdh	T	A	11: 6,292,549 (GRCm39)	Y417N	probably damaging	Het
Or5w19	T	C	2: 87,698,779 (GRCm39)	V148A	probably benign	Het
Ovol1	A	T	19: 5,603,690 (GRCm39)	Y70*	probably null	Het
P2ry1	A	G	3: 60,911,641 (GRCm39)	Y260C	probably damaging	Het
Pcx	G	T	19: 4,653,124 (GRCm39)	R263L	probably damaging	Het
Pla2g4f	T	A	2: 120,131,402 (GRCm39)	T774S	probably benign	Het
Prdm15	T	G	16: 97,622,986 (GRCm39)	K289Q	probably benign	Het
Prl7c1	A	T	13: 27,960,268 (GRCm39)	H91Q	probably benign	Het
Prmt5	C	T	14: 54,745,364 (GRCm39)	R601H	probably benign	Het
Prrc2b	T	A	2: 32,120,637 (GRCm39)	D2192E	probably damaging	Het
Ptdss2	A	G	7: 140,734,372 (GRCm39)	I299V	probably benign	Het
Rbm28	A	G	6: 29,143,591 (GRCm39)	V354A	probably damaging	Het
Rps6kb1	G	C	11: 86,435,484 (GRCm39)		probably null	Het
Sema3f	A	G	9: 107,582,639 (GRCm39)	S35P	probably benign	Het
Serpina3n	A	T	12: 104,375,422 (GRCm39)	T165S	probably benign	Het
Serpinb13	C	T	1: 106,910,574 (GRCm39)	S66L	probably damaging	Het
Sh2d4b	T	A	14: 40,564,389 (GRCm39)	R267*	probably null	Het
Slc5a12	A	T	2: 110,474,769 (GRCm39)	K554*	probably null	Het
Snrnp200	T	C	2: 127,059,334 (GRCm39)	L409P	probably damaging	Het
Snrnp200	T	A	2: 127,069,798 (GRCm39)	V981E	possibly damaging	Het
Spon2	T	A	5: 33,374,682 (GRCm39)	R41S	probably benign	Het
Sptb	A	T	12: 76,630,153 (GRCm39)	M2279K	probably benign	Het
Srcap	T	G	7: 127,140,096 (GRCm39)		probably null	Het
Tctn3	A	G	19: 40,594,186 (GRCm39)	V409A	probably damaging	Het
Tg	A	C	15: 66,554,676 (GRCm39)	Q697P	probably damaging	Het
Tmem181a	A	G	17: 6,340,874 (GRCm39)	D141G	probably benign	Het
Tmem82	A	G	4: 141,341,963 (GRCm39)	S334P	probably benign	Het
Ubr4	A	G	4: 139,151,190 (GRCm39)	Y1875C	probably damaging	Het
Vmn1r63	C	A	7: 5,806,362 (GRCm39)	R90L	probably damaging	Het
Zfp330	A	C	8: 83,497,475 (GRCm39)	Y56D	probably damaging	Het

Other mutations in Npdc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01654:Npdc1	APN	2	25,297,649 (GRCm39)	missense	possibly damaging	0.61
IGL02023:Npdc1	APN	2	25,298,032 (GRCm39)	unclassified	probably benign
IGL02894:Npdc1	APN	2	25,298,007 (GRCm39)	missense	probably benign	0.04
danke	UTSW	2	25,296,257 (GRCm39)	missense	probably damaging	1.00
R0650:Npdc1	UTSW	2	25,298,021 (GRCm39)	missense	probably benign	0.16
R1136:Npdc1	UTSW	2	25,297,727 (GRCm39)	missense	probably benign	0.09
R4008:Npdc1	UTSW	2	25,298,992 (GRCm39)	nonsense	probably null
R4724:Npdc1	UTSW	2	25,298,957 (GRCm39)	missense	probably damaging	1.00
R4725:Npdc1	UTSW	2	25,298,957 (GRCm39)	missense	probably damaging	1.00
R4726:Npdc1	UTSW	2	25,298,957 (GRCm39)	missense	probably damaging	1.00
R4836:Npdc1	UTSW	2	25,298,957 (GRCm39)	missense	probably damaging	1.00
R4843:Npdc1	UTSW	2	25,298,957 (GRCm39)	missense	probably damaging	1.00
R4882:Npdc1	UTSW	2	25,298,957 (GRCm39)	missense	probably damaging	1.00
R5108:Npdc1	UTSW	2	25,298,667 (GRCm39)	missense	probably damaging	1.00
R5393:Npdc1	UTSW	2	25,298,682 (GRCm39)	missense	probably damaging	1.00
R5572:Npdc1	UTSW	2	25,298,957 (GRCm39)	missense	probably damaging	1.00
R5573:Npdc1	UTSW	2	25,298,957 (GRCm39)	missense	probably damaging	1.00
R5574:Npdc1	UTSW	2	25,298,957 (GRCm39)	missense	probably damaging	1.00
R5605:Npdc1	UTSW	2	25,298,957 (GRCm39)	missense	probably damaging	1.00
R5630:Npdc1	UTSW	2	25,298,957 (GRCm39)	missense	probably damaging	1.00
R5632:Npdc1	UTSW	2	25,298,957 (GRCm39)	missense	probably damaging	1.00
R5655:Npdc1	UTSW	2	25,297,692 (GRCm39)	missense	possibly damaging	0.71
R6823:Npdc1	UTSW	2	25,299,121 (GRCm39)	missense	probably damaging	1.00
R7151:Npdc1	UTSW	2	25,299,120 (GRCm39)	missense	probably damaging	0.98
R7400:Npdc1	UTSW	2	25,296,257 (GRCm39)	missense	probably damaging	1.00
R8777:Npdc1	UTSW	2	25,298,129 (GRCm39)	missense	probably damaging	0.98
R8777-TAIL:Npdc1	UTSW	2	25,298,129 (GRCm39)	missense	probably damaging	0.98
R9233:Npdc1	UTSW	2	25,296,329 (GRCm39)	missense	probably damaging	1.00
R9391:Npdc1	UTSW	2	25,297,979 (GRCm39)	missense	possibly damaging	0.72
R9570:Npdc1	UTSW	2	25,298,312 (GRCm39)	missense	probably benign	0.10

Predicted Primers

PCR Primer
(F):5'- TCTGAAGTGGCCGCTTTTC -3'
(R):5'- TCAAACAGTGGGTTGCGCAC -3'

Sequencing Primer
(F):5'- GAAGTGGCCGCTTTTCTCCTG -3'
(R):5'- TGGGTTGCGCACCTCCATC -3'

Posted On

2015-11-11