Mutagenetix > Incidental Mutation

Incidental Mutation 'R4863:Ncdn'

374631

Institutional Source

Beutler Lab

Gene Symbol

Ncdn

Ensembl Gene

ENSMUSG00000028833

Gene Name

neurochondrin

Synonyms

norbin, neurochondrin-1, neurochondrin-2

MMRRC Submission

042473-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4863 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

126743750-126753438 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 126750423 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 202 (L202Q)

Ref Sequence

ENSEMBL: ENSMUSP00000101722 (fasta)

Gene Model

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

AlphaFold

Q9Z0E0

Predicted Effect

probably damaging
Transcript: ENSMUST00000030637
AA Change: L202Q

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

SMART Domains

Protein: ENSMUSP00000030637
Gene: ENSMUSG00000028833
AA Change: L202Q

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

probably damaging
Transcript: ENSMUST00000106116
AA Change: L202Q

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

SMART Domains

Protein: ENSMUSP00000101722
Gene: ENSMUSG00000028833
AA Change: L202Q

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

probably benign
Transcript: ENSMUST00000132660

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136035

Predicted Effect

probably benign
Transcript: ENSMUST00000148935

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

Meta Mutation Damage Score

0.8136

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.2%

Validation Efficiency

99% (105/106)

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: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930578I06Rik	C	T	14: 63,973,209 (GRCm38)	R190H	probably benign	Het
Abcc12	T	A	8: 86,538,376 (GRCm38)	I647F	probably damaging	Het
Acnat2	C	A	4: 49,380,172 (GRCm38)	W384L	probably damaging	Het
Acvr1	A	G	2: 58,477,711 (GRCm38)	L146P	possibly damaging	Het
Ankrd16	T	A	2: 11,784,316 (GRCm38)	M238K	probably benign	Het
Clmn	A	T	12: 104,797,094 (GRCm38)	I91N	probably damaging	Het
Cog8	A	T	8: 107,050,174 (GRCm38)	L523H	probably damaging	Het
Cpxm2	T	A	7: 132,059,747 (GRCm38)	K437M	probably benign	Het
Dhx57	A	T	17: 80,253,111 (GRCm38)	V999E	probably damaging	Het
Dnpep	T	C	1: 75,309,230 (GRCm38)		probably benign	Het
Dok3	G	A	13: 55,523,457 (GRCm38)	R434W	probably damaging	Het
Dpysl5	C	T	5: 30,784,343 (GRCm38)	H275Y	probably benign	Het
Ednra	A	T	8: 77,667,383 (GRCm38)	N361K	probably damaging	Het
Ei24	A	T	9: 36,784,565 (GRCm38)	S210R	probably damaging	Het
Erich3	T	A	3: 154,764,804 (GRCm38)	V158E	unknown	Het
Fam193a	T	A	5: 34,466,205 (GRCm38)	V1379E	possibly damaging	Het
Fasn	A	G	11: 120,808,828 (GRCm38)	V2304A	probably damaging	Het
Fcgbp	A	C	7: 28,086,344 (GRCm38)	D402A	probably benign	Het
Fkbp14	T	C	6: 54,585,945 (GRCm38)		probably benign	Het
Fnip1	G	A	11: 54,515,556 (GRCm38)	V1160I	possibly damaging	Het
Fsd2	T	C	7: 81,552,964 (GRCm38)	K289R	probably null	Het
Fuca2	A	T	10: 13,505,907 (GRCm38)	D188V	probably damaging	Het
Gfpt2	T	C	11: 49,810,970 (GRCm38)	V116A	probably benign	Het
Gm10770	T	A	2: 150,178,896 (GRCm38)	K234*	probably null	Het
Gm9887	A	G	12: 69,371,989 (GRCm38)		probably benign	Het
Gtf3c2	A	G	5: 31,159,233 (GRCm38)		probably benign	Het
H2-M10.3	T	C	17: 36,366,636 (GRCm38)	D250G	probably damaging	Het
Hapln4	G	A	8: 70,084,492 (GRCm38)	V26M	possibly damaging	Het
Hook3	G	A	8: 26,038,029 (GRCm38)	A611V	probably damaging	Het
Hr	T	C	14: 70,571,972 (GRCm38)	L1141P	probably damaging	Het
Ifngr1	T	C	10: 19,609,416 (GRCm38)	S388P	probably damaging	Het
Itga3	T	A	11: 95,061,967 (GRCm38)	Q326L	probably damaging	Het
Itgb3	T	A	11: 104,665,520 (GRCm38)	I729N	probably damaging	Het
Kcnab2	A	G	4: 152,401,946 (GRCm38)	S132P	probably damaging	Het
Lama3	T	C	18: 12,498,678 (GRCm38)		probably benign	Het
Lama3	C	T	18: 12,539,793 (GRCm38)	A2481V	probably damaging	Het
Lce1e	A	T	3: 92,707,871 (GRCm38)	C56*	probably null	Het
Lmcd1	T	C	6: 112,287,871 (GRCm38)		probably benign	Het
Lrrc14	T	A	15: 76,713,362 (GRCm38)		probably null	Het
Lypd8l	A	T	11: 58,612,512 (GRCm38)		probably null	Het
Map4k5	G	A	12: 69,818,438 (GRCm38)	P591L	probably benign	Het
Mapk13	C	A	17: 28,776,310 (GRCm38)	D168E	probably damaging	Het
Marf1	A	C	16: 14,132,665 (GRCm38)	H952Q	possibly damaging	Het
Megf6	T	C	4: 154,254,281 (GRCm38)		probably null	Het
Mical3	T	C	6: 121,033,787 (GRCm38)	I411M	probably damaging	Het
Myo5a	A	T	9: 75,217,507 (GRCm38)	K1781N	probably damaging	Het
N4bp2	T	C	5: 65,808,130 (GRCm38)	V1174A	probably benign	Het
Ncor1	T	A	11: 62,392,638 (GRCm38)	M408L	possibly damaging	Het
Nf1	T	C	11: 79,409,409 (GRCm38)	L249P	probably damaging	Het
Nlrp9b	T	A	7: 20,049,596 (GRCm38)		probably null	Het
Nxpe3	A	T	16: 55,849,633 (GRCm38)	Y370N	probably damaging	Het
P2rx2	T	A	5: 110,341,568 (GRCm38)	T167S	probably benign	Het
Pcdhb19	G	T	18: 37,499,108 (GRCm38)	R652L	probably benign	Het
Pcdhga12	T	C	18: 37,768,281 (GRCm38)	L722P	probably benign	Het
Pde6a	A	T	18: 61,245,592 (GRCm38)	I329F	probably damaging	Het
Pdpr	T	A	8: 111,101,951 (GRCm38)	S29T	probably benign	Het
Pfkfb3	T	C	2: 11,486,312 (GRCm38)	D173G	probably benign	Het
Plcd4	A	G	1: 74,565,802 (GRCm38)		probably null	Het
Polr1g	T	A	7: 19,357,759 (GRCm38)	Q141L	probably damaging	Het
Pou2f2	A	G	7: 25,097,108 (GRCm38)		probably benign	Het
Ppp1r14c	TGGCGGCGGCGGCGGCGG	TGGCGGCGGCGGCGG	10: 3,366,702 (GRCm38)		probably benign	Het
Ppp1r42	T	C	1: 10,003,386 (GRCm38)		probably benign	Het
Ptpre	C	T	7: 135,669,132 (GRCm38)	H346Y	probably benign	Het
Ptpro	T	A	6: 137,443,594 (GRCm38)	V1007D	probably damaging	Het
Rab12	A	T	17: 66,498,108 (GRCm38)	Y142N	probably damaging	Het
Rai14	A	C	15: 10,572,470 (GRCm38)	M857R	probably damaging	Het
Ranbp2	A	G	10: 58,492,421 (GRCm38)	K2753R	probably damaging	Het
Rasa4	A	T	5: 136,103,911 (GRCm38)	K6*	probably null	Het
Rasgef1a	A	G	6: 118,089,139 (GRCm38)	M438V	probably benign	Het
Recql	T	G	6: 142,359,006 (GRCm38)		probably benign	Het
Rftn2	A	G	1: 55,172,039 (GRCm38)	V425A	probably benign	Het
Ror1	A	G	4: 100,409,804 (GRCm38)	Y234C	probably damaging	Het
Sap30l	T	A	11: 57,806,054 (GRCm38)	L70Q	probably damaging	Het
Scn4a	T	C	11: 106,320,002 (GRCm38)	R1730G	probably damaging	Het
Serinc5	T	G	13: 92,690,980 (GRCm38)	I268R	probably damaging	Het
Sin3b	G	A	8: 72,744,948 (GRCm38)	V432I	possibly damaging	Het
Slc30a6	T	C	17: 74,412,654 (GRCm38)	M203T	possibly damaging	Het
Soat1	T	C	1: 156,432,328 (GRCm38)	N481S	probably damaging	Het
Sos2	G	A	12: 69,640,154 (GRCm38)	T206I	probably benign	Het
Sp100	G	T	1: 85,705,003 (GRCm38)	A132S	probably benign	Het
Sp140l1	C	T	1: 85,088,800 (GRCm38)		probably benign	Het
Spata31d1c	T	A	13: 65,035,790 (GRCm38)	L382*	probably null	Het
Stard9	T	A	2: 120,700,860 (GRCm38)	W2533R	probably benign	Het
Tas2r126	A	G	6: 42,435,390 (GRCm38)	T286A	probably benign	Het
Tedc2	T	A	17: 24,217,936 (GRCm38)	K275M	probably damaging	Het
Ten1	A	T	11: 116,218,231 (GRCm38)	K242N	probably benign	Het
Thoc2l	A	T	5: 104,517,750 (GRCm38)	D46V	possibly damaging	Het
Tial1	C	T	7: 128,455,028 (GRCm38)	V1I	probably damaging	Het
Tle2	G	A	10: 81,588,891 (GRCm38)	R649H	possibly damaging	Het
Tmem178	A	G	17: 80,944,945 (GRCm38)	D86G	probably benign	Het
Trim29	T	A	9: 43,329,575 (GRCm38)	D528E	possibly damaging	Het
Vmn2r61	A	T	7: 42,300,708 (GRCm38)	T851S	probably benign	Het
Vmn2r72	T	A	7: 85,750,598 (GRCm38)	Q414H	possibly damaging	Het
Yars1	A	T	4: 129,189,882 (GRCm38)		probably benign	Het
Yipf4	A	G	17: 74,494,092 (GRCm38)	Q135R	probably damaging	Het
Zfp341	G	A	2: 154,645,866 (GRCm38)		probably benign	Het
Zfp426	T	C	9: 20,470,038 (GRCm38)	Y536C	probably damaging	Het
Zp2	T	G	7: 120,135,772 (GRCm38)	Y430S	probably damaging	Het

Other mutations in Ncdn

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00340:Ncdn	APN	4	126,747,188 (GRCm38)	missense	probably benign	0.00
R0031:Ncdn	UTSW	4	126,750,108 (GRCm38)	splice site	probably null
R0135:Ncdn	UTSW	4	126,746,669 (GRCm38)	missense	probably benign	0.37
R0413:Ncdn	UTSW	4	126,750,534 (GRCm38)	missense	possibly damaging	0.52
R1404:Ncdn	UTSW	4	126,750,040 (GRCm38)	missense	probably benign	0.33
R1404:Ncdn	UTSW	4	126,750,040 (GRCm38)	missense	probably benign	0.33
R1486:Ncdn	UTSW	4	126,748,598 (GRCm38)	missense	probably damaging	1.00
R1533:Ncdn	UTSW	4	126,748,698 (GRCm38)	nonsense	probably null
R1785:Ncdn	UTSW	4	126,745,273 (GRCm38)	critical splice acceptor site	probably null
R1786:Ncdn	UTSW	4	126,745,273 (GRCm38)	critical splice acceptor site	probably null
R1789:Ncdn	UTSW	4	126,752,003 (GRCm38)	missense	probably damaging	1.00
R1791:Ncdn	UTSW	4	126,751,939 (GRCm38)	critical splice donor site	probably null
R3406:Ncdn	UTSW	4	126,748,595 (GRCm38)	missense	probably benign	0.09
R4547:Ncdn	UTSW	4	126,746,674 (GRCm38)	missense	probably damaging	1.00
R4916:Ncdn	UTSW	4	126,749,938 (GRCm38)	missense	possibly damaging	0.89
R4917:Ncdn	UTSW	4	126,749,938 (GRCm38)	missense	possibly damaging	0.89
R4918:Ncdn	UTSW	4	126,749,938 (GRCm38)	missense	possibly damaging	0.89
R5218:Ncdn	UTSW	4	126,750,810 (GRCm38)	missense	probably benign	0.13
R5356:Ncdn	UTSW	4	126,747,228 (GRCm38)	missense	probably damaging	1.00
R5617:Ncdn	UTSW	4	126,745,047 (GRCm38)	missense	probably damaging	0.99
R5718:Ncdn	UTSW	4	126,749,950 (GRCm38)	nonsense	probably null
R6057:Ncdn	UTSW	4	126,745,031 (GRCm38)	missense	probably benign	0.05
R6343:Ncdn	UTSW	4	126,747,171 (GRCm38)	missense	possibly damaging	0.74
R6986:Ncdn	UTSW	4	126,747,229 (GRCm38)	missense	probably damaging	1.00
R6988:Ncdn	UTSW	4	126,747,189 (GRCm38)	missense	probably benign	0.00
R8257:Ncdn	UTSW	4	126,749,883 (GRCm38)	critical splice donor site	probably null
R8279:Ncdn	UTSW	4	126,750,406 (GRCm38)	missense	probably benign	0.00
R8804:Ncdn	UTSW	4	126,750,105 (GRCm38)	missense	probably benign	0.09
R8812:Ncdn	UTSW	4	126,745,112 (GRCm38)	missense	possibly damaging	0.52
R9047:Ncdn	UTSW	4	126,750,828 (GRCm38)	missense	possibly damaging	0.69
R9206:Ncdn	UTSW	4	126,750,248 (GRCm38)	missense	probably benign	0.03
R9208:Ncdn	UTSW	4	126,750,248 (GRCm38)	missense	probably benign	0.03
R9289:Ncdn	UTSW	4	126,750,110 (GRCm38)	missense	possibly damaging	0.81
R9353:Ncdn	UTSW	4	126,750,671 (GRCm38)	missense	probably benign	0.00
R9420:Ncdn	UTSW	4	126,751,969 (GRCm38)	missense	probably damaging	1.00
R9578:Ncdn	UTSW	4	126,752,002 (GRCm38)	missense	probably damaging	1.00
R9687:Ncdn	UTSW	4	126,748,674 (GRCm38)	missense	probably damaging	1.00
R9698:Ncdn	UTSW	4	126,749,895 (GRCm38)	missense	probably damaging	1.00
R9778:Ncdn	UTSW	4	126,748,674 (GRCm38)	missense	probably damaging	1.00
R9781:Ncdn	UTSW	4	126,748,674 (GRCm38)	missense	probably damaging	1.00
Z1176:Ncdn	UTSW	4	126,750,153 (GRCm38)	missense	probably benign	0.05
Z1176:Ncdn	UTSW	4	126,750,151 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGATCTCGGTGGCATTCAGG -3'
(R):5'- AGGTCCTGAACAAGATCCCC -3'

Sequencing Primer
(F):5'- CATTCAGGGGGCACAGTTG -3'
(R):5'- ACATTCCTTACAGCCCGGG -3'

Posted On

2016-03-17