Mutagenetix > Incidental Mutation

Incidental Mutation 'R0135:Ncdn'

21867

Institutional Source

Beutler Lab

Gene Symbol

Ncdn

Ensembl Gene

ENSMUSG00000028833

Gene Name

neurochondrin

Synonyms

neurochondrin-2, neurochondrin-1, norbin

MMRRC Submission

038420-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0135 (G1)

Quality Score

225

Status

Validated (trace)

Chromosome

Chromosomal Location

126637543-126647231 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 126640462 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 544 (S544T)

Ref Sequence

ENSEMBL: ENSMUSP00000101722 (fasta)

Gene Model

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

AlphaFold

Q9Z0E0

Predicted Effect

probably benign
Transcript: ENSMUST00000030637
AA Change: S544T

PolyPhen 2 Score 0.373 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000030637
Gene: ENSMUSG00000028833
AA Change: S544T

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: ENSMUST00000106116
AA Change: S544T

PolyPhen 2 Score 0.373 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000101722
Gene: ENSMUSG00000028833
AA Change: S544T

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

Meta Mutation Damage Score

0.1819

Coding Region Coverage

1x: 99.0%
3x: 98.3%
10x: 96.5%
20x: 93.6%

Validation Efficiency

100% (80/80)

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932438H23Rik	A	G	16: 90,852,515 (GRCm39)	F207S	probably damaging	Het
Abhd8	T	A	8: 71,910,718 (GRCm39)	K363N	probably benign	Het
Adam11	T	A	11: 102,667,399 (GRCm39)	V653E	probably damaging	Het
Adam18	T	C	8: 25,155,558 (GRCm39)	S154G	possibly damaging	Het
Adamts1	T	C	16: 85,595,591 (GRCm39)		probably benign	Het
Afm	G	T	5: 90,698,181 (GRCm39)	V528L	probably benign	Het
Alox12b	C	T	11: 69,053,574 (GRCm39)	H145Y	probably benign	Het
Ankmy2	C	A	12: 36,220,434 (GRCm39)		probably benign	Het
Aox3	G	A	1: 58,164,247 (GRCm39)		probably benign	Het
Arhgap28	T	C	17: 68,171,583 (GRCm39)	D396G	probably damaging	Het
B430203G13Rik	T	C	12: 17,974,489 (GRCm39)		noncoding transcript	Het
Bean1	C	T	8: 104,943,807 (GRCm39)	P121S	probably damaging	Het
Bok	T	C	1: 93,614,229 (GRCm39)	S21P	probably damaging	Het
Brwd1	A	C	16: 95,848,304 (GRCm39)	N572K	probably damaging	Het
C5ar1	A	T	7: 15,982,864 (GRCm39)	V52E	probably damaging	Het
Cblif	G	T	19: 11,735,118 (GRCm39)	C246F	probably damaging	Het
Cdr2l	C	A	11: 115,284,497 (GRCm39)	P278T	probably damaging	Het
Cnga4	T	A	7: 105,056,055 (GRCm39)	I219N	probably damaging	Het
Cpne2	C	T	8: 95,281,553 (GRCm39)		probably benign	Het
D430041D05Rik	A	G	2: 104,085,379 (GRCm39)	S1057P	possibly damaging	Het
Def8	G	A	8: 124,183,234 (GRCm39)	A278T	probably damaging	Het
Dgcr2	A	G	16: 17,676,306 (GRCm39)	S152P	probably damaging	Het
Dstyk	A	T	1: 132,390,672 (GRCm39)	D828V	probably damaging	Het
Eml2	T	C	7: 18,937,877 (GRCm39)	S582P	probably damaging	Het
Engase	T	C	11: 118,375,304 (GRCm39)	Y359H	possibly damaging	Het
Fat3	T	C	9: 15,918,073 (GRCm39)	D1450G	probably damaging	Het
Fbxw8	A	T	5: 118,208,552 (GRCm39)	I467N	probably damaging	Het
Fhdc1	A	T	3: 84,352,925 (GRCm39)	Y767N	probably damaging	Het
Flii	T	C	11: 60,614,204 (GRCm39)	D105G	probably damaging	Het
Gaa	C	T	11: 119,169,716 (GRCm39)	T590I	probably benign	Het
Gabrr1	T	A	4: 33,160,224 (GRCm39)	S303T	probably damaging	Het
Garre1	T	C	7: 33,945,382 (GRCm39)	I499M	probably damaging	Het
Glp1r	A	G	17: 31,143,551 (GRCm39)	I196V	probably benign	Het
Grm6	G	A	11: 50,744,050 (GRCm39)	E174K	probably damaging	Het
Helz2	A	C	2: 180,874,062 (GRCm39)	L2144R	probably damaging	Het
Itpr1	A	T	6: 108,465,443 (GRCm39)		probably benign	Het
Kcns1	A	T	2: 164,006,875 (GRCm39)	S363T	possibly damaging	Het
Kif13a	A	T	13: 46,947,419 (GRCm39)	V855E	probably damaging	Het
Krt42	T	C	11: 100,153,985 (GRCm39)	T424A	possibly damaging	Het
Lct	A	T	1: 128,212,860 (GRCm39)	F1931Y	probably damaging	Het
Lrp1b	A	T	2: 41,159,251 (GRCm39)	V1563E	probably damaging	Het
Lrrc37	C	A	11: 103,508,873 (GRCm39)		probably benign	Het
Lzts2	T	C	19: 45,014,626 (GRCm39)		probably benign	Het
Mamdc4	C	T	2: 25,456,932 (GRCm39)	R615Q	possibly damaging	Het
Mei1	C	T	15: 81,956,170 (GRCm39)	Q133*	probably null	Het
Mif4gd	T	C	11: 115,499,291 (GRCm39)	E197G	probably damaging	Het
Nfat5	C	T	8: 108,065,707 (GRCm39)	R156W	probably damaging	Het
Or52a5	T	A	7: 103,426,970 (GRCm39)	D194V	probably damaging	Het
Padi6	T	C	4: 140,464,663 (GRCm39)	T114A	probably benign	Het
Pigk	G	T	3: 152,450,343 (GRCm39)		probably benign	Het
Pkd1	T	A	17: 24,784,045 (GRCm39)	F197Y	possibly damaging	Het
Pld5	A	T	1: 175,798,155 (GRCm39)	F415I	probably damaging	Het
Pnpla5	A	G	15: 83,998,150 (GRCm39)	L364P	probably damaging	Het
Prrc2c	G	A	1: 162,543,052 (GRCm39)		probably benign	Het
Rab32	C	T	10: 10,426,584 (GRCm39)	D121N	probably damaging	Het
Rab44	A	T	17: 29,357,106 (GRCm39)	T79S	probably benign	Het
Reln	G	T	5: 22,333,647 (GRCm39)	N258K	probably damaging	Het
Retsat	A	G	6: 72,579,755 (GRCm39)	T177A	probably damaging	Het
Serpinf2	T	A	11: 75,327,219 (GRCm39)	H236L	probably damaging	Het
Slc26a6	A	T	9: 108,737,794 (GRCm39)		probably benign	Het
Slitrk1	T	A	14: 109,149,061 (GRCm39)	E550V	probably benign	Het
Smarcd3	A	T	5: 24,800,497 (GRCm39)		probably benign	Het
Spdye4a	A	C	5: 143,210,857 (GRCm39)		probably null	Het
Susd2	C	T	10: 75,474,348 (GRCm39)	G572D	probably damaging	Het
Tcaf3	C	T	6: 42,566,692 (GRCm39)	R799K	probably benign	Het
Tg	A	G	15: 66,566,719 (GRCm39)	S1256G	probably benign	Het
Them4	A	T	3: 94,230,877 (GRCm39)		probably benign	Het
Tmem210	C	T	2: 25,178,480 (GRCm39)	A47V	probably damaging	Het
Tnfrsf1b	A	G	4: 144,955,616 (GRCm39)	Y47H	probably benign	Het
Tnik	T	G	3: 28,661,394 (GRCm39)	N598K	possibly damaging	Het
Ttc3	A	G	16: 94,263,127 (GRCm39)	N1498D	possibly damaging	Het
Ttll4	C	A	1: 74,719,087 (GRCm39)	H313N	possibly damaging	Het
Vipr2	A	G	12: 116,106,447 (GRCm39)	I348V	probably benign	Het
Vps13a	A	G	19: 16,758,129 (GRCm39)	V2A	probably damaging	Het
Vps72	G	A	3: 95,026,508 (GRCm39)	R151K	probably damaging	Het
Zfp106	A	G	2: 120,350,968 (GRCm39)	V1561A	probably damaging	Het
Zfp658	C	A	7: 43,223,019 (GRCm39)	Y431*	probably null	Het
Zkscan2	T	C	7: 123,079,864 (GRCm39)	K698E	possibly damaging	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
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
R4918: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'- AAAGCGGAGGCTTACACTCCGAAC -3'
(R):5'- CAGCTCAGCTACTTGGCATCTGAC -3'

Sequencing Primer
(F):5'- GCTTACACTCCGAACACTGC -3'
(R):5'- ATCTGACTGACCCAGATGGC -3'

Posted On

2013-04-12