Mutagenetix > Incidental Mutation

Incidental Mutation 'R5574:Npdc1'

437084

Institutional Source

Beutler Lab

Gene Symbol

Npdc1

Ensembl Gene

ENSMUSG00000015094

Gene Name

neural proliferation, differentiation and control 1

Synonyms

NPDC-1

MMRRC Submission

043129-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5574 (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: 99.9%
3x: 99.7%
10x: 98.7%
20x: 96.6%

Validation Efficiency

99% (68/69)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700129C05Rik	T	A	14: 59,380,205 (GRCm39)	N31I	possibly damaging	Het
Acvr1b	T	A	15: 101,099,958 (GRCm39)	M304K	probably benign	Het
Adamts1	G	T	16: 85,596,530 (GRCm39)	D106E	probably damaging	Het
Atosa	A	T	9: 74,917,672 (GRCm39)	D757V	probably damaging	Het
Blm	C	A	7: 80,149,521 (GRCm39)	C696F	probably damaging	Het
Bnip3l-ps	T	A	12: 18,267,119 (GRCm39)		noncoding transcript	Het
Ccdc171	A	T	4: 83,611,990 (GRCm39)	N895I	probably damaging	Het
Cdhr4	A	T	9: 107,870,527 (GRCm39)		probably benign	Het
Cfap97	T	C	8: 46,623,179 (GRCm39)	S190P	probably damaging	Het
Chrnb1	A	C	11: 69,684,509 (GRCm39)		probably benign	Het
Clns1a	A	G	7: 97,370,165 (GRCm39)		probably benign	Het
Col8a2	G	A	4: 126,205,061 (GRCm39)		probably benign	Het
Cr2	T	A	1: 194,823,544 (GRCm39)	E721V	probably damaging	Het
Csk	A	G	9: 57,536,584 (GRCm39)	V172A	probably benign	Het
Cyp2g1	G	A	7: 26,520,165 (GRCm39)	V466M	possibly damaging	Het
Cyp4f13	A	G	17: 33,148,179 (GRCm39)	Y349H	probably benign	Het
Dnm1l	T	C	16: 16,147,685 (GRCm39)	Y205C	probably damaging	Het
Dync1i2	A	T	2: 71,063,994 (GRCm39)	T113S	probably benign	Het
Edem2	T	C	2: 155,558,075 (GRCm39)	E186G	probably damaging	Het
Eya2	G	A	2: 165,605,736 (GRCm39)	R380H	probably damaging	Het
Gldn	A	G	9: 54,220,206 (GRCm39)	T132A	probably damaging	Het
Gm13941	A	T	2: 110,930,951 (GRCm39)	I74K	unknown	Het
Gm3898	C	T	9: 43,741,339 (GRCm39)		noncoding transcript	Het
Ighmbp2	C	T	19: 3,321,536 (GRCm39)	V408I	probably benign	Het
Klhdc10	C	T	6: 30,439,864 (GRCm39)	L127F	possibly damaging	Het
Letm1	G	A	5: 33,926,730 (GRCm39)	T189M	possibly damaging	Het
Lrrc17	A	T	5: 21,775,355 (GRCm39)	I306F	possibly damaging	Het
Lrrk2	T	A	15: 91,671,219 (GRCm39)	V2000E	probably damaging	Het
Mettl9	A	T	7: 120,647,093 (GRCm39)	E66D	probably benign	Het
Mroh1	T	A	15: 76,318,131 (GRCm39)	V877D	probably benign	Het
Mycbp2	C	T	14: 103,380,203 (GRCm39)	V3760M	possibly damaging	Het
Nos3	A	G	5: 24,573,859 (GRCm39)	T208A	possibly damaging	Het
Obp2a	A	T	2: 25,590,842 (GRCm39)	T70S	possibly damaging	Het
Or4a72	C	T	2: 89,405,321 (GRCm39)	V250I	possibly damaging	Het
Or52a5b	T	G	7: 103,417,323 (GRCm39)	I94L	possibly damaging	Het
Or5al6	T	C	2: 85,976,535 (GRCm39)	D181G	probably damaging	Het
Or8b8	A	T	9: 37,808,877 (GRCm39)	Y59F	probably damaging	Het
Or8h10	A	G	2: 86,808,867 (GRCm39)	V91A	probably benign	Het
Pate2	A	G	9: 35,597,411 (GRCm39)		probably benign	Het
Pdzph1	A	G	17: 59,280,942 (GRCm39)	F447L	probably benign	Het
Pias1	A	G	9: 62,827,775 (GRCm39)	C211R	probably damaging	Het
Plb1	A	G	5: 32,487,291 (GRCm39)	S929G	probably benign	Het
Pramel32	T	G	4: 88,546,280 (GRCm39)	E354A	probably benign	Het
Prc1	G	A	7: 79,944,290 (GRCm39)		probably benign	Het
Prex2	A	G	1: 11,210,282 (GRCm39)	D574G	probably damaging	Het
Rapgef4	G	A	2: 71,864,464 (GRCm39)		probably null	Het
Rmc1	CTGTGTGTT	CTGTGTGTTGTGTGTT	18: 12,318,063 (GRCm39)		probably null	Het
Rock2	T	C	12: 17,011,642 (GRCm39)	M690T	possibly damaging	Het
Sinhcaf	C	T	6: 148,846,378 (GRCm39)		probably benign	Het
Slc18a2	A	G	19: 59,249,837 (GRCm39)	I25V	probably benign	Het
Slc9a5	T	A	8: 106,091,323 (GRCm39)	I701K	probably benign	Het
Sorcs1	T	A	19: 50,210,571 (GRCm39)	N765Y	probably damaging	Het
Ssh2	A	T	11: 77,340,941 (GRCm39)	I698L	probably benign	Het
Stam	A	G	2: 14,120,675 (GRCm39)	D58G	probably damaging	Het
Thsd4	C	A	9: 59,879,683 (GRCm39)	R1018L	probably damaging	Het
Tnxb	A	G	17: 34,929,998 (GRCm39)	T2911A	probably benign	Het
Trpm7	A	C	2: 126,654,950 (GRCm39)	F1329L	probably benign	Het
Ttll9	A	G	2: 152,826,168 (GRCm39)	E126G	possibly damaging	Het
Tubgcp5	G	A	7: 55,455,077 (GRCm39)	V258M	probably benign	Het
Unc45a	G	A	7: 79,984,604 (GRCm39)	A232V	probably damaging	Het
Utp14b	G	A	1: 78,644,126 (GRCm39)	V675M	probably damaging	Het
Vmn2r67	T	A	7: 84,801,099 (GRCm39)	H279L	probably benign	Het
Vmn2r75	G	T	7: 85,815,510 (GRCm39)	A118E	probably benign	Het
Wdr36	A	T	18: 32,999,012 (GRCm39)	Q886L	probably damaging	Het
Zfp433	T	A	10: 81,555,125 (GRCm39)	Y27*	probably null	Het
Zfp715	A	T	7: 42,960,463 (GRCm39)	S43T	possibly damaging	Het
Zfyve26	A	G	12: 79,286,698 (GRCm39)	S2297P	possibly 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
R4728: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
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'- TGAAGTGGCCGCTTTTCTC -3'
(R):5'- TGGTCAAACAGTGGGTTGC -3'

Sequencing Primer
(F):5'- GTCCCTACCTGCTCGAAAC -3'
(R):5'- AAACAGTGGGTTGCGCACC -3'

Posted On

2016-10-26