Mutagenetix > Incidental Mutation

Incidental Mutation 'R5108:Npdc1'

393641

Institutional Source

Beutler Lab

Gene Symbol

Npdc1

Ensembl Gene

ENSMUSG00000015094

Gene Name

neural proliferation, differentiation and control 1

Synonyms

NPDC-1

MMRRC Submission

042696-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5108 (G1)

Quality Score

176

Status

Validated

Chromosome

Chromosomal Location

25293062-25299506 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 25298667 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Tyrosine at position 260 (H260Y)

Ref Sequence

ENSEMBL: ENSMUSP00000071387 (fasta)

Gene Model

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

AlphaFold

Q64322

Predicted Effect

probably damaging
Transcript: ENSMUST00000055921
AA Change: H269Y

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000049602
Gene: ENSMUSG00000015094
AA Change: H269Y

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000071442
AA Change: H260Y

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

SMART Domains

Protein: ENSMUSP00000071387
Gene: ENSMUSG00000015094
AA Change: H260Y

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

probably damaging
Transcript: ENSMUST00000133409
AA Change: H202Y

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000117773
Gene: ENSMUSG00000015094
AA Change: H202Y

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136138

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156824

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138651

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144413

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141106

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

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

Meta Mutation Damage Score

0.5080

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.3%
20x: 92.5%

Validation Efficiency

99% (79/80)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aass	T	A	6: 23,094,207 (GRCm39)	N94Y	probably damaging	Het
Ak2	A	G	4: 128,896,034 (GRCm39)	T104A	probably damaging	Het
Alox12b	G	T	11: 69,048,208 (GRCm39)	A46S	probably benign	Het
Ank1	G	T	8: 23,622,571 (GRCm39)	V1662F	probably benign	Het
Anxa3	T	C	5: 96,978,273 (GRCm39)	I219T	possibly damaging	Het
Aoc1l3	C	T	6: 48,965,504 (GRCm39)	T504I	probably damaging	Het
Arhgap40	G	A	2: 158,389,599 (GRCm39)	V588M	probably damaging	Het
Arhgef38	T	C	3: 132,843,029 (GRCm39)	T514A	probably benign	Het
Ascl4	C	A	10: 85,764,422 (GRCm39)	A23E	probably benign	Het
Bcl11b	T	C	12: 107,931,985 (GRCm39)	T196A	probably benign	Het
C1ra	A	T	6: 124,499,881 (GRCm39)	Y689F	probably damaging	Het
Ccr3	A	G	9: 123,828,968 (GRCm39)	N101S	probably benign	Het
Cep70	A	T	9: 99,145,865 (GRCm39)		probably null	Het
Ces1b	A	G	8: 93,798,541 (GRCm39)	V215A	probably damaging	Het
Cndp1	A	T	18: 84,650,186 (GRCm39)	I169N	probably damaging	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Het
Fbxo2	A	G	4: 148,250,486 (GRCm39)	Q275R	probably damaging	Het
Fbxo44	T	C	4: 148,243,020 (GRCm39)	N133S	probably damaging	Het
Fzr1	C	T	10: 81,205,284 (GRCm39)		probably benign	Het
Grn	T	C	11: 102,325,228 (GRCm39)	S213P	probably benign	Het
Ifi203	A	T	1: 173,751,580 (GRCm39)	C414S	probably damaging	Het
Igfn1	C	T	1: 135,910,179 (GRCm39)	R135H	probably benign	Het
Kcnk10	T	C	12: 98,401,560 (GRCm39)	M358V	probably benign	Het
Kcnn2	A	T	18: 45,725,122 (GRCm39)	Y471F	probably damaging	Het
Klhl20	A	T	1: 160,926,820 (GRCm39)	V391E	probably damaging	Het
Krt1c	C	T	15: 101,721,721 (GRCm39)	G440D	possibly damaging	Het
Lpin1	A	T	12: 16,623,716 (GRCm39)	Y223N	probably benign	Het
Luzp2	G	A	7: 54,915,038 (GRCm39)	C321Y	probably damaging	Het
Mcm3ap	T	C	10: 76,338,536 (GRCm39)	V1388A	probably benign	Het
Mdga2	A	T	12: 66,533,515 (GRCm39)	H223Q	probably benign	Het
Mgat4e	G	T	1: 134,468,961 (GRCm39)	P361Q	probably benign	Het
Mylk3	A	T	8: 86,085,721 (GRCm39)	I208N	possibly damaging	Het
Myom2	T	A	8: 15,182,667 (GRCm39)	V1368E	probably damaging	Het
Mypn	C	T	10: 62,972,073 (GRCm39)	D656N	probably damaging	Het
Nat10	C	A	2: 103,562,548 (GRCm39)	R596L	probably damaging	Het
Nek8	T	C	11: 78,063,353 (GRCm39)	D137G	probably damaging	Het
Neurl1a	A	G	19: 47,246,074 (GRCm39)	K552E	probably damaging	Het
Nuggc	A	T	14: 65,876,129 (GRCm39)	I581F	probably damaging	Het
Or8d23	T	A	9: 38,842,151 (GRCm39)	I228N	probably damaging	Het
P2rx6	T	C	16: 17,380,037 (GRCm39)	Y54H	probably damaging	Het
Pcmtd2	A	G	2: 181,486,216 (GRCm39)	E112G	probably damaging	Het
Pcnx4	G	A	12: 72,620,855 (GRCm39)	V892I	probably benign	Het
Pdss1	T	A	2: 22,796,895 (GRCm39)	V136E	possibly damaging	Het
Pias3	T	C	3: 96,612,253 (GRCm39)	L561P	possibly damaging	Het
Pomgnt1	G	A	4: 116,013,453 (GRCm39)		probably benign	Het
Scn2a	C	T	2: 65,518,974 (GRCm39)	T400I	probably damaging	Het
Sec24d	T	A	3: 123,099,434 (GRCm39)		probably null	Het
Sftpb	T	G	6: 72,281,640 (GRCm39)	L11R	probably damaging	Het
Slc22a19	A	G	19: 7,688,536 (GRCm39)	I8T	probably benign	Het
Slc22a30	A	G	19: 8,363,790 (GRCm39)	S266P	probably damaging	Het
Slc36a2	C	A	11: 55,050,214 (GRCm39)	G465W	probably damaging	Het
Slc4a2	G	A	5: 24,644,331 (GRCm39)	M976I	probably damaging	Het
Smcr8	C	T	11: 60,670,696 (GRCm39)	Q615*	probably null	Het
Sobp	T	C	10: 43,036,815 (GRCm39)	E41G	probably damaging	Het
Spopfm1	C	T	3: 94,173,142 (GRCm39)	S50L	probably damaging	Het
Spz1	A	T	13: 92,711,554 (GRCm39)	C307*	probably null	Het
Sult1d1	C	T	5: 87,711,728 (GRCm39)		probably null	Het
Tas2r110	T	C	6: 132,845,668 (GRCm39)	M233T	probably damaging	Het
Tmc3	C	A	7: 83,269,156 (GRCm39)	S781R	probably damaging	Het
Tmem234	G	T	4: 129,495,730 (GRCm39)		probably benign	Het
Trpm3	A	T	19: 22,882,078 (GRCm39)	Q645L	probably benign	Het
Ttn	C	A	2: 76,565,055 (GRCm39)	V28391F	probably damaging	Het
Txnrd3	G	T	6: 89,650,016 (GRCm39)	A425S	probably benign	Het
Ubr1	C	T	2: 120,793,903 (GRCm39)	G94R	probably benign	Het
Ufl1	A	G	4: 25,269,026 (GRCm39)		probably null	Het
Utp20	T	C	10: 88,604,735 (GRCm39)	D1720G	probably benign	Het
Vmn1r13	T	A	6: 57,186,901 (GRCm39)	M20K	probably benign	Het
Vmn1r61	A	G	7: 5,613,519 (GRCm39)	I265T	probably benign	Het
Zfp120	T	C	2: 149,961,862 (GRCm39)	T29A	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
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
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'- AGAAGGCTGACTATGCTGCC -3'
(R):5'- TCAATGTATTGCTGCCCTGG -3'

Sequencing Primer
(F):5'- CTGGAACTCACTTTGTAGACCAGG -3'
(R):5'- AATGTATTGCTGCCCTGGGTAGG -3'

Posted On

2016-06-15