Mutagenetix > Incidental Mutation

Incidental Mutation 'R4918:Ncdn'

378389

Institutional Source

Beutler Lab

Gene Symbol

Ncdn

Ensembl Gene

ENSMUSG00000028833

Gene Name

neurochondrin

Synonyms

neurochondrin-2, neurochondrin-1, norbin

MMRRC Submission

042520-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4918 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

126637543-126647231 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 126643731 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Phenylalanine at position 364 (L364F)

Ref Sequence

ENSEMBL: ENSMUSP00000101722 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030637] [ENSMUST00000047431] [ENSMUST00000102607] [ENSMUST00000102608] [ENSMUST00000106116] [ENSMUST00000154640] [ENSMUST00000148935] [ENSMUST00000132660]

AlphaFold

Q9Z0E0

Predicted Effect

possibly damaging
Transcript: ENSMUST00000030637
AA Change: L364F

PolyPhen 2 Score 0.893 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000030637
Gene: ENSMUSG00000028833
AA Change: L364F

Domain	Start	End	E-Value	Type
Pfam:Neurochondrin	30	637	3e-209	PFAM
low complexity region	649	659	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000047431

SMART Domains

Protein: ENSMUSP00000037802
Gene: ENSMUSG00000028830

Domain	Start	End	E-Value	Type
low complexity region	83	97	N/A	INTRINSIC
FN3	113	391	8.45e1	SMART
IG_like	305	398	3.57e1	SMART
PKD	309	400	3.1e-1	SMART
FN3	399	485	2.7e1	SMART
PKD	408	497	1.87e-4	SMART
FN3	502	676	4.47e1	SMART
PKD	503	593	3.22e-8	SMART
IG_like	508	591	1.17e1	SMART
IG_like	597	782	1.66e2	SMART
PKD	599	687	8.98e-7	SMART
PKD	693	784	1.05e-7	SMART
FN3	694	772	3.71e1	SMART
transmembrane domain	927	949	N/A	INTRINSIC
low complexity region	995	1010	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000102607

SMART Domains

Protein: ENSMUSP00000099667
Gene: ENSMUSG00000028830

Domain	Start	End	E-Value	Type
low complexity region	83	97	N/A	INTRINSIC
FN3	113	391	8.45e1	SMART
IG_like	305	398	3.57e1	SMART
PKD	309	400	3.1e-1	SMART
FN3	399	485	2.7e1	SMART
PKD	408	497	1.87e-4	SMART
FN3	502	676	4.47e1	SMART
PKD	503	593	3.22e-8	SMART
IG_like	508	591	1.17e1	SMART
IG_like	597	782	1.66e2	SMART
PKD	599	687	8.98e-7	SMART
PKD	693	784	1.05e-7	SMART
FN3	694	772	3.71e1	SMART
transmembrane domain	927	949	N/A	INTRINSIC
low complexity region	995	1010	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000102608

SMART Domains

Protein: ENSMUSP00000099668
Gene: ENSMUSG00000028830

Domain	Start	End	E-Value	Type
low complexity region	83	97	N/A	INTRINSIC
FN3	113	391	8.45e1	SMART
IG_like	305	398	3.57e1	SMART
PKD	309	400	3.1e-1	SMART
FN3	399	485	2.7e1	SMART
PKD	408	497	1.87e-4	SMART
FN3	502	676	4.47e1	SMART
PKD	503	593	3.22e-8	SMART
IG_like	508	591	1.17e1	SMART
IG_like	597	782	1.66e2	SMART
PKD	599	687	8.98e-7	SMART
PKD	693	784	1.05e-7	SMART
FN3	694	772	3.71e1	SMART
transmembrane domain	927	949	N/A	INTRINSIC
low complexity region	995	1010	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000106116
AA Change: L364F

PolyPhen 2 Score 0.893 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000101722
Gene: ENSMUSG00000028833
AA Change: L364F

Domain	Start	End	E-Value	Type
Pfam:Neurochondrin	30	637	9.1e-217	PFAM
low complexity region	649	659	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127079

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131900

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136035

Predicted Effect

probably benign
Transcript: ENSMUST00000154640

SMART Domains

Protein: ENSMUSP00000122352
Gene: ENSMUSG00000028830

Domain	Start	End	E-Value	Type
low complexity region	83	97	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000148935

Predicted Effect

probably benign
Transcript: ENSMUST00000132660

Meta Mutation Damage Score

0.2488

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.4%
20x: 92.7%

Validation Efficiency

99% (116/117)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a leucine-rich cytoplasmic protein, which is highly similar to a mouse protein that negatively regulates Ca/calmodulin-dependent protein kinase II phosphorylation and may be essential for spatial learning processes. Several alternatively spliced transcript variants of this gene have been described. [provided by RefSeq, Jul 2008]
PHENOTYPE: Targeted inactivation of this gene results in early embryonic lethality in the homozygous state and impaired chondrocyte proliferation and differentiation in the heterozygous state. Gene trap mutation resulted in lacrimal gland hypertrophy. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 102 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca6	T	A	11: 110,071,377 (GRCm39)	I1492F	probably damaging	Het
Ago4	A	C	4: 126,400,635 (GRCm39)	C693G	probably damaging	Het
Apobec2	T	C	17: 48,730,153 (GRCm39)	E171G	probably benign	Het
Arfgef3	T	A	10: 18,492,638 (GRCm39)	I1258F	probably damaging	Het
Arhgef40	A	G	14: 52,227,556 (GRCm39)	E434G	probably damaging	Het
Baz2b	T	A	2: 59,744,387 (GRCm39)	T1373S	possibly damaging	Het
Bcas1	T	C	2: 170,220,806 (GRCm39)	D324G	probably damaging	Het
Bdp1	A	T	13: 100,191,713 (GRCm39)	V1422E	probably damaging	Het
Bfsp1	C	T	2: 143,669,391 (GRCm39)	R396Q	probably benign	Het
Bnip1	C	T	17: 27,002,525 (GRCm39)		probably benign	Het
Bnip5	T	G	17: 29,127,337 (GRCm39)	Q224P	probably benign	Het
Bpifb9b	T	A	2: 154,156,026 (GRCm39)		probably null	Het
Casp8	T	C	1: 58,866,377 (GRCm39)	F126S	probably damaging	Het
Cdh26	T	C	2: 178,091,614 (GRCm39)	S58P	probably benign	Het
Cntnap2	T	C	6: 46,506,969 (GRCm39)		probably benign	Het
Col9a1	T	C	1: 24,276,339 (GRCm39)	I749T	possibly damaging	Het
Ddx50	A	T	10: 62,463,450 (GRCm39)	C414*	probably null	Het
Defb42	A	G	14: 63,285,790 (GRCm39)	I57V	probably benign	Het
Dennd5a	A	G	7: 109,500,296 (GRCm39)	F943S	probably damaging	Het
Dhx40	G	T	11: 86,695,217 (GRCm39)	H98N	possibly damaging	Het
Disp2	A	T	2: 118,620,935 (GRCm39)	S556C	probably damaging	Het
Dpysl5	T	G	5: 30,949,612 (GRCm39)	F461V	probably damaging	Het
Efcab11	T	C	12: 99,685,321 (GRCm39)	D151G	probably damaging	Het
Egfem1	T	C	3: 29,206,042 (GRCm39)	V93A	probably damaging	Het
Ehbp1	T	C	11: 22,096,592 (GRCm39)	D299G	probably benign	Het
Esyt2	T	C	12: 116,287,760 (GRCm39)	V226A	probably benign	Het
Fan1	A	T	7: 64,023,286 (GRCm39)		probably benign	Het
Fasn	T	G	11: 120,707,472 (GRCm39)	N799T	probably benign	Het
Fbxo3	T	G	2: 103,885,311 (GRCm39)	N388K	probably damaging	Het
Fer1l4	T	C	2: 155,873,220 (GRCm39)	K1287E	probably benign	Het
Fn1	A	T	1: 71,634,968 (GRCm39)		probably null	Het
Fsip2	G	A	2: 82,824,114 (GRCm39)	V6616I	possibly damaging	Het
Fut8	G	T	12: 77,521,818 (GRCm39)	A486S	probably damaging	Het
Glp2r	G	T	11: 67,648,419 (GRCm39)	Y94*	probably null	Het
Gm10764	A	G	10: 87,126,579 (GRCm39)		noncoding transcript	Het
Gm6788	C	T	19: 28,740,664 (GRCm39)		noncoding transcript	Het
Gm8122	T	C	14: 43,091,573 (GRCm39)	N65S	unknown	Het
Golga4	C	A	9: 118,387,213 (GRCm39)	S1445Y	probably damaging	Het
Gsdmd	A	G	15: 75,736,241 (GRCm39)	I123M	probably benign	Het
Hsf4	A	G	8: 105,999,367 (GRCm39)	E235G	probably benign	Het
Ifi206	T	A	1: 173,309,610 (GRCm39)	T129S	possibly damaging	Het
Jakmip1	G	A	5: 37,248,619 (GRCm39)	R93Q	probably damaging	Het
Kcnj1	T	A	9: 32,308,056 (GRCm39)	L160Q	probably damaging	Het
Kif1a	T	A	1: 93,002,700 (GRCm39)	E233V	probably benign	Het
Krt5	A	T	15: 101,618,742 (GRCm39)	Y340N	probably damaging	Het
Krt90	T	A	15: 101,470,914 (GRCm39)	H116L	possibly damaging	Het
Large2	A	G	2: 92,196,452 (GRCm39)		probably benign	Het
Marchf4	T	G	1: 72,467,938 (GRCm39)	S365R	probably benign	Het
Mei4	A	G	9: 81,772,216 (GRCm39)	T10A	probably benign	Het
Meis1	T	C	11: 18,959,222 (GRCm39)		probably benign	Het
Mllt1	T	C	17: 57,206,813 (GRCm39)	T344A	probably benign	Het
Mrps28	A	G	3: 8,947,614 (GRCm39)		probably benign	Het
Nckap1l	A	G	15: 103,392,040 (GRCm39)	N825S	probably benign	Het
Nfat5	T	A	8: 108,051,284 (GRCm39)	D47E	probably damaging	Het
Nfix	T	C	8: 85,498,458 (GRCm39)	I172V	probably benign	Het
Nkx3-1	G	A	14: 69,428,367 (GRCm39)	G72S	probably benign	Het
Nsf	G	A	11: 103,801,185 (GRCm39)		probably benign	Het
Or1b1	A	T	2: 36,995,170 (GRCm39)	I164N	possibly damaging	Het
Or1n1b	A	G	2: 36,780,344 (GRCm39)	I172T	probably damaging	Het
Or3a1b	A	T	11: 74,012,705 (GRCm39)	I197F	probably benign	Het
Or51g2	A	T	7: 102,622,614 (GRCm39)	I195N	possibly damaging	Het
Or5ak20	C	T	2: 85,183,632 (GRCm39)	V213I	probably benign	Het
Or5b106	T	A	19: 13,123,355 (GRCm39)	I223L	possibly damaging	Het
Or5bw2	C	T	7: 6,573,643 (GRCm39)	L218F	possibly damaging	Het
Or9g10	T	C	2: 85,584,465 (GRCm39)		probably benign	Het
Pcdh20	A	C	14: 88,705,104 (GRCm39)	L732R	probably damaging	Het
Pgbd5	C	A	8: 125,097,305 (GRCm39)	K408N	probably benign	Het
Pip4k2c	T	C	10: 127,035,196 (GRCm39)	T391A	possibly damaging	Het
Ppm1k	T	A	6: 57,487,762 (GRCm39)	N354Y	probably damaging	Het
Prpf18	T	C	2: 4,641,981 (GRCm39)	D186G	probably benign	Het
Rab3gap1	T	A	1: 127,816,914 (GRCm39)	W58R	possibly damaging	Het
Rbp3	T	C	14: 33,677,368 (GRCm39)	Y439H	probably damaging	Het
Rere	T	A	4: 150,703,601 (GRCm39)	W1528R	probably damaging	Het
Rsf1	T	C	7: 97,311,612 (GRCm39)	S781P	probably damaging	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Ryr2	A	G	13: 11,609,872 (GRCm39)	V753A	probably damaging	Het
Schip1	A	T	3: 68,315,818 (GRCm39)		probably benign	Het
Scin	T	A	12: 40,119,373 (GRCm39)	I552F	possibly damaging	Het
Scn3a	T	C	2: 65,291,799 (GRCm39)	N1649S	probably damaging	Het
Sh3rf3	A	T	10: 58,842,925 (GRCm39)	D297V	probably damaging	Het
Slc20a2	C	T	8: 23,051,020 (GRCm39)	S351L	probably damaging	Het
Slc35e2	C	A	4: 155,700,693 (GRCm39)	P272Q	probably damaging	Het
Slc4a1	A	G	11: 102,243,279 (GRCm39)	V784A	probably damaging	Het
Slco1b2	G	A	6: 141,615,096 (GRCm39)	V334I	probably benign	Het
Slf2	T	G	19: 44,960,100 (GRCm39)	D1022E	probably damaging	Het
Spag6	A	T	2: 18,750,360 (GRCm39)	I469F	probably benign	Het
Spsb2	A	C	6: 124,786,711 (GRCm39)	E148A	probably benign	Het
Sulf1	A	G	1: 12,888,720 (GRCm39)	D335G	probably damaging	Het
Tchhl1	A	G	3: 93,377,623 (GRCm39)	D109G	possibly damaging	Het
Thoc7	T	C	14: 13,953,154 (GRCm38)	I83V	probably damaging	Het
Thsd7a	A	C	6: 12,327,558 (GRCm39)	I1438S	probably damaging	Het
Tm4sf1	C	T	3: 57,200,448 (GRCm39)	G85S	probably damaging	Het
Tmem63a	T	A	1: 180,794,086 (GRCm39)	I541N	probably benign	Het
Trav6d-4	T	C	14: 52,991,240 (GRCm39)	F95S	probably damaging	Het
Ttn	A	T	2: 76,641,587 (GRCm39)	L5176Q	possibly damaging	Het
Ttn	T	C	2: 76,589,598 (GRCm39)	T21219A	probably damaging	Het
Unc80	T	C	1: 66,685,709 (GRCm39)	Y2278H	possibly damaging	Het
Usp8	A	T	2: 126,562,060 (GRCm39)	K85*	probably null	Het
Vmn2r69	T	A	7: 85,055,967 (GRCm39)	M724L	probably benign	Het
Zeb2	A	G	2: 44,886,894 (GRCm39)	I706T	probably damaging	Het
Zfp512	T	C	5: 31,634,209 (GRCm39)	S407P	probably damaging	Het
Zfp791	T	A	8: 85,837,580 (GRCm39)	I95L	probably benign	Het

Other mutations in Ncdn

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00340:Ncdn	APN	4	126,640,981 (GRCm39)	missense	probably benign	0.00
R0031:Ncdn	UTSW	4	126,643,901 (GRCm39)	splice site	probably null
R0135:Ncdn	UTSW	4	126,640,462 (GRCm39)	missense	probably benign	0.37
R0413:Ncdn	UTSW	4	126,644,327 (GRCm39)	missense	possibly damaging	0.52
R1404:Ncdn	UTSW	4	126,643,833 (GRCm39)	missense	probably benign	0.33
R1404:Ncdn	UTSW	4	126,643,833 (GRCm39)	missense	probably benign	0.33
R1486:Ncdn	UTSW	4	126,642,391 (GRCm39)	missense	probably damaging	1.00
R1533:Ncdn	UTSW	4	126,642,491 (GRCm39)	nonsense	probably null
R1785:Ncdn	UTSW	4	126,639,066 (GRCm39)	critical splice acceptor site	probably null
R1786:Ncdn	UTSW	4	126,639,066 (GRCm39)	critical splice acceptor site	probably null
R1789:Ncdn	UTSW	4	126,645,796 (GRCm39)	missense	probably damaging	1.00
R1791:Ncdn	UTSW	4	126,645,732 (GRCm39)	critical splice donor site	probably null
R3406:Ncdn	UTSW	4	126,642,388 (GRCm39)	missense	probably benign	0.09
R4547:Ncdn	UTSW	4	126,640,467 (GRCm39)	missense	probably damaging	1.00
R4863:Ncdn	UTSW	4	126,644,216 (GRCm39)	missense	probably damaging	1.00
R4916:Ncdn	UTSW	4	126,643,731 (GRCm39)	missense	possibly damaging	0.89
R4917:Ncdn	UTSW	4	126,643,731 (GRCm39)	missense	possibly damaging	0.89
R5218:Ncdn	UTSW	4	126,644,603 (GRCm39)	missense	probably benign	0.13
R5356:Ncdn	UTSW	4	126,641,021 (GRCm39)	missense	probably damaging	1.00
R5617:Ncdn	UTSW	4	126,638,840 (GRCm39)	missense	probably damaging	0.99
R5718:Ncdn	UTSW	4	126,643,743 (GRCm39)	nonsense	probably null
R6057:Ncdn	UTSW	4	126,638,824 (GRCm39)	missense	probably benign	0.05
R6343:Ncdn	UTSW	4	126,640,964 (GRCm39)	missense	possibly damaging	0.74
R6986:Ncdn	UTSW	4	126,641,022 (GRCm39)	missense	probably damaging	1.00
R6988:Ncdn	UTSW	4	126,640,982 (GRCm39)	missense	probably benign	0.00
R8257:Ncdn	UTSW	4	126,643,676 (GRCm39)	critical splice donor site	probably null
R8279:Ncdn	UTSW	4	126,644,199 (GRCm39)	missense	probably benign	0.00
R8804:Ncdn	UTSW	4	126,643,898 (GRCm39)	missense	probably benign	0.09
R8812:Ncdn	UTSW	4	126,638,905 (GRCm39)	missense	possibly damaging	0.52
R9047:Ncdn	UTSW	4	126,644,621 (GRCm39)	missense	possibly damaging	0.69
R9206:Ncdn	UTSW	4	126,644,041 (GRCm39)	missense	probably benign	0.03
R9208:Ncdn	UTSW	4	126,644,041 (GRCm39)	missense	probably benign	0.03
R9289:Ncdn	UTSW	4	126,643,903 (GRCm39)	missense	possibly damaging	0.81
R9353:Ncdn	UTSW	4	126,644,464 (GRCm39)	missense	probably benign	0.00
R9420:Ncdn	UTSW	4	126,645,762 (GRCm39)	missense	probably damaging	1.00
R9578:Ncdn	UTSW	4	126,645,795 (GRCm39)	missense	probably damaging	1.00
R9687:Ncdn	UTSW	4	126,642,467 (GRCm39)	missense	probably damaging	1.00
R9698:Ncdn	UTSW	4	126,643,688 (GRCm39)	missense	probably damaging	1.00
R9778:Ncdn	UTSW	4	126,642,467 (GRCm39)	missense	probably damaging	1.00
R9781:Ncdn	UTSW	4	126,642,467 (GRCm39)	missense	probably damaging	1.00
Z1176:Ncdn	UTSW	4	126,643,946 (GRCm39)	missense	probably benign	0.05
Z1176:Ncdn	UTSW	4	126,643,944 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCCAGGCTGATATGTGAGAC -3'
(R):5'- TCTGGGAGCAAGTTTCTGGC -3'

Sequencing Primer
(F):5'- CAGAACAGTCTGCTTCGACTTGG -3'
(R):5'- TGGCCCTGCTCGTGAATCTAG -3'

Posted On

2016-04-15