Mutagenetix > Incidental Mutation

Incidental Mutation 'R1486:Ncdn'

163454

Institutional Source

Beutler Lab

Gene Symbol

Ncdn

Ensembl Gene

ENSMUSG00000028833

Gene Name

neurochondrin

Synonyms

norbin, neurochondrin-1, neurochondrin-2

MMRRC Submission

039539-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R1486 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

126743750-126753438 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 126748598 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Aspartic acid at position 422 (V422D)

Ref Sequence

ENSEMBL: ENSMUSP00000101722 (fasta)

Gene Model

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

AlphaFold

Q9Z0E0

Predicted Effect

probably damaging
Transcript: ENSMUST00000030637
AA Change: V422D

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000030637
Gene: ENSMUSG00000028833
AA Change: V422D

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: 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: V422D

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000101722
Gene: ENSMUSG00000028833
AA Change: V422D

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

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

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.4%
20x: 93.1%

Validation Efficiency

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930402H24Rik	A	G	2: 130,737,418	L633P	probably damaging	Het
4930430A15Rik	T	G	2: 111,200,358	Q402P	possibly damaging	Het
4933425L06Rik	T	C	13: 105,109,783	V284A	probably benign	Het
A730015C16Rik	A	G	4: 108,847,946	E19G	probably benign	Het
A730018C14Rik	T	C	12: 112,415,695		noncoding transcript	Het
Acrbp	T	A	6: 125,050,622	Y78N	probably damaging	Het
Adamtsl4	T	C	3: 95,681,856	S422G	probably benign	Het
Apba2	T	C	7: 64,736,948	V429A	probably damaging	Het
Atf6	A	G	1: 170,794,691	C454R	probably damaging	Het
Bhlhe40	T	C	6: 108,664,929	I278T	probably damaging	Het
Birc6	G	T	17: 74,639,820	V2845L	probably damaging	Het
Card11	T	C	5: 140,876,519	I1008V	probably benign	Het
Catsperg1	C	A	7: 29,185,495	K900N	probably damaging	Het
Chek2	T	G	5: 110,841,227		probably benign	Het
Dnah9	A	T	11: 65,834,272	S4352T	probably damaging	Het
Eif3c	C	T	7: 126,564,721	R50Q	probably damaging	Het
Eml6	A	C	11: 29,805,114	I887S	possibly damaging	Het
Fopnl	A	G	16: 14,300,140	V172A	probably benign	Het
Gipc1	C	T	8: 83,661,179	Q63*	probably null	Het
Grm4	A	G	17: 27,434,717	L706P	probably damaging	Het
Irak3	T	C	10: 120,143,061	D495G	probably damaging	Het
Itga9	T	G	9: 118,626,450	V64G	probably damaging	Het
Iws1	T	C	18: 32,097,256	I759T	probably damaging	Het
Kdm3b	T	A	18: 34,834,304	F1721I	probably damaging	Het
Lrrc8c	T	A	5: 105,607,529	V390E	probably damaging	Het
Mki67	G	A	7: 135,699,720	T1195I	probably benign	Het
Mphosph8	C	T	14: 56,689,039	T646I	probably damaging	Het
Nrg1	T	C	8: 31,818,344	E548G	probably damaging	Het
Nup37	T	C	10: 88,148,254	Y11H	probably damaging	Het
Olfr1062	T	A	2: 86,423,481	H65L	probably damaging	Het
Olfr1377	G	A	11: 50,984,781	V27I	probably benign	Het
Olfr585	A	T	7: 103,098,430	I230F	probably damaging	Het
Olfr601	T	A	7: 103,358,994	M67L	possibly damaging	Het
Pcgf1	T	G	6: 83,079,126	S70R	probably damaging	Het
Prps1l3	C	T	12: 57,238,787	A121V	probably benign	Het
Rasal1	T	C	5: 120,654,852	Y57H	probably damaging	Het
Rbm12b2	A	G	4: 12,094,841	R567G	probably benign	Het
Rep15	T	A	6: 147,033,079	F139I	probably damaging	Het
Ros1	T	C	10: 52,172,858	Y92C	probably damaging	Het
Sin3b	A	G	8: 72,750,513	T803A	probably benign	Het
Skint11	G	A	4: 114,194,818		probably null	Het
Sobp	T	G	10: 43,022,522	S356R	probably benign	Het
Spats2l	T	C	1: 57,900,811	I228T	probably damaging	Het
Sqor	G	A	2: 122,807,645		probably null	Het
Stox1	T	C	10: 62,664,636	D715G	probably benign	Het
Tln2	C	A	9: 67,311,839	G275W	probably damaging	Het
Tmc5	C	T	7: 118,673,432	P942S	probably benign	Het
Tor4a	A	T	2: 25,194,679	I404N	possibly damaging	Het
Ttc3	G	A	16: 94,448,129	R1162Q	probably damaging	Het
Zfp451	T	C	1: 33,777,727	K164E	probably damaging	Het

Other mutations in Ncdn

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00340:Ncdn	APN	4	126747188	missense	probably benign	0.00
R0031:Ncdn	UTSW	4	126750108	splice site	probably null
R0135:Ncdn	UTSW	4	126746669	missense	probably benign	0.37
R0413:Ncdn	UTSW	4	126750534	missense	possibly damaging	0.52
R1404:Ncdn	UTSW	4	126750040	missense	probably benign	0.33
R1404:Ncdn	UTSW	4	126750040	missense	probably benign	0.33
R1533:Ncdn	UTSW	4	126748698	nonsense	probably null
R1785:Ncdn	UTSW	4	126745273	critical splice acceptor site	probably null
R1786:Ncdn	UTSW	4	126745273	critical splice acceptor site	probably null
R1789:Ncdn	UTSW	4	126752003	missense	probably damaging	1.00
R1791:Ncdn	UTSW	4	126751939	critical splice donor site	probably null
R3406:Ncdn	UTSW	4	126748595	missense	probably benign	0.09
R4547:Ncdn	UTSW	4	126746674	missense	probably damaging	1.00
R4863:Ncdn	UTSW	4	126750423	missense	probably damaging	1.00
R4916:Ncdn	UTSW	4	126749938	missense	possibly damaging	0.89
R4917:Ncdn	UTSW	4	126749938	missense	possibly damaging	0.89
R4918:Ncdn	UTSW	4	126749938	missense	possibly damaging	0.89
R5218:Ncdn	UTSW	4	126750810	missense	probably benign	0.13
R5356:Ncdn	UTSW	4	126747228	missense	probably damaging	1.00
R5617:Ncdn	UTSW	4	126745047	missense	probably damaging	0.99
R5718:Ncdn	UTSW	4	126749950	nonsense	probably null
R6057:Ncdn	UTSW	4	126745031	missense	probably benign	0.05
R6343:Ncdn	UTSW	4	126747171	missense	possibly damaging	0.74
R6986:Ncdn	UTSW	4	126747229	missense	probably damaging	1.00
R6988:Ncdn	UTSW	4	126747189	missense	probably benign	0.00
R8257:Ncdn	UTSW	4	126749883	critical splice donor site	probably null
R8279:Ncdn	UTSW	4	126750406	missense	probably benign	0.00
R8804:Ncdn	UTSW	4	126750105	missense	probably benign	0.09
R8812:Ncdn	UTSW	4	126745112	missense	possibly damaging	0.52
R9047:Ncdn	UTSW	4	126750828	missense	possibly damaging	0.69
R9206:Ncdn	UTSW	4	126750248	missense	probably benign	0.03
R9208:Ncdn	UTSW	4	126750248	missense	probably benign	0.03
R9289:Ncdn	UTSW	4	126750110	missense	possibly damaging	0.81
R9353:Ncdn	UTSW	4	126750671	missense	probably benign	0.00
R9420:Ncdn	UTSW	4	126751969	missense	probably damaging	1.00
R9578:Ncdn	UTSW	4	126752002	missense	not run
Z1176:Ncdn	UTSW	4	126750151	missense	probably damaging	1.00
Z1176:Ncdn	UTSW	4	126750153	missense	probably benign	0.05

Predicted Primers

PCR Primer
(F):5'- ATGACATCAGGAGCCCAGGTTAGG -3'
(R):5'- AGTTCTGTTACTGGCAGGCAGAGG -3'

Sequencing Primer
(F):5'- ccatccatccatccatccatc -3'
(R):5'- AGCAGAAAGAGCCCTTTGTG -3'

Posted On

2014-03-28