Mutagenetix > Incidental Mutation

Incidental Mutation 'R4726:Npdc1'

358439

Institutional Source

Beutler Lab

Gene Symbol

Npdc1

Ensembl Gene

ENSMUSG00000015094

Gene Name

neural proliferation, differentiation and control 1

Synonyms

NPDC-1

MMRRC Submission

041989-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4726 (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: 98.6%
10x: 97.1%
20x: 94.8%

Validation Efficiency

99% (74/75)

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930583I09Rik	T	C	17: 65,141,448 (GRCm39)	S52G	probably null	Het
Abcc2	T	C	19: 43,820,553 (GRCm39)	S1351P	probably benign	Het
Acp2	T	A	2: 91,034,622 (GRCm39)	L87Q	probably damaging	Het
Adgrl3	C	A	5: 81,794,425 (GRCm39)	T550K	possibly damaging	Het
Amotl2	A	G	9: 102,601,018 (GRCm39)	R329G	probably benign	Het
Angel1	T	C	12: 86,768,649 (GRCm39)	N278S	probably damaging	Het
Ankrd12	A	C	17: 66,277,319 (GRCm39)	M1985R	probably damaging	Het
Apob	T	A	12: 8,040,267 (GRCm39)	F535I	probably damaging	Het
Art3	A	G	5: 92,559,002 (GRCm39)	K313R	probably benign	Het
Asxl2	C	T	12: 3,551,872 (GRCm39)	H1205Y	possibly damaging	Het
Bsph1	A	T	7: 13,206,920 (GRCm39)	M99L	probably benign	Het
Ccdc153	T	C	9: 44,154,963 (GRCm39)		probably null	Het
Cdh16	A	T	8: 105,342,664 (GRCm39)	M28K	probably damaging	Het
Cdhr2	T	C	13: 54,866,352 (GRCm39)	F353L	probably damaging	Het
Chrna2	G	T	14: 66,386,345 (GRCm39)	V164L	possibly damaging	Het
Cip2a	A	G	16: 48,834,433 (GRCm39)	T672A	probably benign	Het
Ckmt1	T	C	2: 121,191,712 (GRCm39)		probably null	Het
Col25a1	A	T	3: 130,313,430 (GRCm39)	E280V	possibly damaging	Het
Dnajc12	A	G	10: 63,233,087 (GRCm39)	D76G	probably damaging	Het
Drd3	G	T	16: 43,643,164 (GRCm39)	E467*	probably null	Het
Ecpas	A	G	4: 58,844,191 (GRCm39)	V525A	probably damaging	Het
Ehbp1l1	C	A	19: 5,769,204 (GRCm39)	A700S	possibly damaging	Het
Gab1	T	C	8: 81,515,682 (GRCm39)	D212G	possibly damaging	Het
Gm26996	A	G	6: 130,557,134 (GRCm39)		noncoding transcript	Het
Gm28113	A	G	15: 75,198,577 (GRCm39)		noncoding transcript	Het
Has3	T	C	8: 107,604,718 (GRCm39)	F308S	probably damaging	Het
Ifit3b	T	A	19: 34,588,860 (GRCm39)	I12N	probably benign	Het
Ifna4	C	A	4: 88,760,519 (GRCm39)	T141K	probably benign	Het
Ints3	A	G	3: 90,301,084 (GRCm39)	S840P	probably damaging	Het
Itih4	T	C	14: 30,611,792 (GRCm39)	V132A	probably damaging	Het
Itprid2	T	A	2: 79,493,101 (GRCm39)	I1216N	probably damaging	Het
Kcnj10	A	G	1: 172,196,639 (GRCm39)	Y51C	probably damaging	Het
Klk1b24	G	A	7: 43,839,820 (GRCm39)	V60I	probably damaging	Het
Klra14-ps	C	A	6: 130,134,626 (GRCm39)		noncoding transcript	Het
Krt6b	A	G	15: 101,586,520 (GRCm39)	I323T	probably damaging	Het
Lilra5	A	C	7: 4,240,957 (GRCm39)	Q17P	probably benign	Het
Lrrc7	GAAGTTGTTTGGAGATTCTTATCTTA	GA	3: 158,024,045 (GRCm39)		probably benign	Het
Map3k4	T	C	17: 12,451,851 (GRCm39)	N1479S	possibly damaging	Het
Mbd3l2	A	T	9: 18,356,256 (GRCm39)	I194F	probably damaging	Het
Megf10	T	C	18: 57,420,864 (GRCm39)	I834T	probably benign	Het
Mterf4	G	A	1: 93,229,471 (GRCm39)	T251M	probably damaging	Het
Mtmr3	A	T	11: 4,457,634 (GRCm39)	D170E	probably damaging	Het
Myom3	C	T	4: 135,534,586 (GRCm39)		probably null	Het
Nemp1	G	A	10: 127,530,462 (GRCm39)	V305I	probably benign	Het
Nlrp1b	G	T	11: 71,072,232 (GRCm39)	T537K	probably benign	Het
Or5b3	T	A	19: 13,388,469 (GRCm39)	C179S	probably damaging	Het
Or6c206	A	G	10: 129,097,045 (GRCm39)	T72A	possibly damaging	Het
Or8k28	A	G	2: 86,286,580 (GRCm39)	F12L	possibly damaging	Het
Pias1	A	G	9: 62,827,771 (GRCm39)	V212A	probably damaging	Het
Plscr1	T	A	9: 92,145,221 (GRCm39)	V77D	probably damaging	Het
Plxna1	T	C	6: 89,299,798 (GRCm39)	N1657S	probably damaging	Het
Ptprf	A	G	4: 118,069,414 (GRCm39)	V1551A	possibly damaging	Het
Ptprn2	C	A	12: 117,211,393 (GRCm39)	Y857*	probably null	Het
Puf60	A	T	15: 75,944,183 (GRCm39)		probably null	Het
Rnf20	C	T	4: 49,654,579 (GRCm39)	R879*	probably null	Het
Robo1	G	A	16: 72,768,931 (GRCm39)	A499T	probably damaging	Het
Slc39a14	A	G	14: 70,551,048 (GRCm39)		probably null	Het
Smarcad1	A	T	6: 65,052,025 (GRCm39)	H6L	probably damaging	Het
Smg5	A	G	3: 88,243,758 (GRCm39)	S10G	possibly damaging	Het
Stk39	T	A	2: 68,093,647 (GRCm39)	D488V	probably damaging	Het
Stx19	A	G	16: 62,642,495 (GRCm39)	N104D	probably benign	Het
Tcstv1b	A	T	13: 120,635,173 (GRCm39)	S152C	possibly damaging	Het
Tmem222	T	C	4: 133,004,975 (GRCm39)	M21V	probably benign	Het
Trim43b	T	A	9: 88,971,538 (GRCm39)	N205I	possibly damaging	Het
Ubr4	C	A	4: 139,209,890 (GRCm39)	H5017N	possibly damaging	Het
Vmn2r93	A	G	17: 18,536,960 (GRCm39)	T548A	probably damaging	Het
Vps8	G	A	16: 21,267,154 (GRCm39)		probably null	Het
Wasl	A	G	6: 24,633,110 (GRCm39)	V176A	probably benign	Het
Wbp2nl	T	A	15: 82,190,255 (GRCm39)	V61E	probably damaging	Het
Zfp959	T	A	17: 56,205,260 (GRCm39)		probably null	Het
Zmiz1	T	C	14: 25,644,098 (GRCm39)		probably null	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
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
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'- AAGTGGCCGCTTTTCTCCTG -3'
(R):5'- TCAAACAGTGGGTTGCGCAC -3'

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

Posted On

2015-11-11