Mutagenetix > Incidental Mutation

Incidental Mutation 'R7872:Clcn2'

608206

Institutional Source

Beutler Lab

Gene Symbol

Clcn2

Ensembl Gene

ENSMUSG00000022843

Gene Name

chloride channel, voltage-sensitive 2

Synonyms

nmf240, Clc2, ClC-2

MMRRC Submission

045924-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.641) question?

Stock #

R7872 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

20521714-20536496 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 20527210 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Threonine at position 629 (M629T)

Ref Sequence

ENSEMBL: ENSMUSP00000007207 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000007207] [ENSMUST00000120099] [ENSMUST00000131522] [ENSMUST00000232309]

AlphaFold

Q9R0A1

Predicted Effect

probably damaging
Transcript: ENSMUST00000007207
AA Change: M629T

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000007207
Gene: ENSMUSG00000022843
AA Change: M629T

Domain	Start	End	E-Value	Type
low complexity region	2	14	N/A	INTRINSIC
low complexity region	102	111	N/A	INTRINSIC
Pfam:Voltage_CLC	151	555	1.2e-94	PFAM
Blast:CBS	595	644	3e-12	BLAST
low complexity region	666	680	N/A	INTRINSIC
CBS	803	850	3.69e0	SMART
low complexity region	869	881	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000120099
AA Change: M612T

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000112759
Gene: ENSMUSG00000022843
AA Change: M612T

Domain	Start	End	E-Value	Type
low complexity region	2	14	N/A	INTRINSIC
low complexity region	102	111	N/A	INTRINSIC
Pfam:Voltage_CLC	151	538	5.6e-77	PFAM
Blast:CBS	578	627	4e-12	BLAST
low complexity region	649	663	N/A	INTRINSIC
CBS	786	833	3.69e0	SMART
low complexity region	852	864	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000131522

SMART Domains

Protein: ENSMUSP00000122921
Gene: ENSMUSG00000022843

Domain	Start	End	E-Value	Type
low complexity region	2	14	N/A	INTRINSIC
low complexity region	102	111	N/A	INTRINSIC
Pfam:Voltage_CLC	151	473	4.2e-63	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000231381

Predicted Effect

probably damaging
Transcript: ENSMUST00000232309
AA Change: M585T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a voltage-gated chloride channel. The encoded protein is a transmembrane protein that maintains chloride ion homeostasis in various cells. Defects in this gene may be a cause of certain epilepsies. Four transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]
PHENOTYPE: Mice homozygous for a null allele exhibit abnormal brain morphology, male infertility, and abnormal eye morphology. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acta2	C	T	19: 34,220,839 (GRCm39)	D290N	probably damaging	Het
Adam18	T	C	8: 25,101,116 (GRCm39)	D682G	probably benign	Het
Ankrd46	A	G	15: 36,485,989 (GRCm39)	V88A	possibly damaging	Het
Ankub1	T	A	3: 57,572,807 (GRCm39)	K305I	probably damaging	Het
Atrn	T	A	2: 130,812,147 (GRCm39)		probably null	Het
Bambi	A	T	18: 3,511,406 (GRCm39)	T76S	probably benign	Het
Cacna1a	T	A	8: 85,310,283 (GRCm39)	V1447E	probably damaging	Het
Calcoco2	GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC	GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC	11: 95,990,808 (GRCm39)		probably benign	Het
Clcn4	T	C	7: 7,290,780 (GRCm39)	N673S	probably benign	Het
Col20a1	T	C	2: 180,628,371 (GRCm39)	F15S	probably benign	Het
Col2a1	G	A	15: 97,898,458 (GRCm39)	Q39*	probably null	Het
Creb3	A	G	4: 43,563,332 (GRCm39)	E119G	probably benign	Het
Dnah5	A	C	15: 28,245,830 (GRCm39)	D556A	probably damaging	Het
Edar	C	T	10: 58,446,348 (GRCm39)	M192I	possibly damaging	Het
Fam91a1	A	G	15: 58,320,209 (GRCm39)	M634V	probably benign	Het
Fbxo10	C	T	4: 45,051,699 (GRCm39)	V471I	not run	Het
Fer1l5	T	C	1: 36,460,967 (GRCm39)	F2032L	probably benign	Het
Gm5150	A	C	3: 16,060,485 (GRCm39)	M1R	probably null	Het
Grin1	T	C	2: 25,188,202 (GRCm39)	E509G	probably benign	Het
Igkv10-94	C	T	6: 68,681,913 (GRCm39)		probably benign	Het
Il18bp	A	G	7: 101,666,002 (GRCm39)	Y59H	possibly damaging	Het
Ints8	A	T	4: 11,254,062 (GRCm39)	C17S	probably benign	Het
Kcnmb1	T	C	11: 33,916,275 (GRCm39)	Y74H	probably damaging	Het
Kpna1	T	C	16: 35,843,565 (GRCm39)	V313A	probably benign	Het
Lrp4	C	T	2: 91,321,061 (GRCm39)	T1029I	possibly damaging	Het
Lrrc7	A	T	3: 158,059,099 (GRCm39)	C3S	probably damaging	Het
Lyst	C	A	13: 13,810,450 (GRCm39)	H707N	probably benign	Het
Map3k20	A	G	2: 72,202,098 (GRCm39)	K148R	probably damaging	Het
Mcidas	G	A	13: 113,135,521 (GRCm39)	G315S	probably damaging	Het
Miip	C	T	4: 147,947,375 (GRCm39)	G236S	probably benign	Het
Mocs1	T	A	17: 49,746,561 (GRCm39)	I177N	probably damaging	Het
Muc5b	A	G	7: 141,399,850 (GRCm39)	D441G	unknown	Het
Ncoa1	T	C	12: 4,328,186 (GRCm39)	N884S	probably benign	Het
Or12j4	A	G	7: 140,046,696 (GRCm39)	N194S	probably damaging	Het
Or51a39	A	G	7: 102,363,389 (GRCm39)	V77A	probably benign	Het
Padi6	A	T	4: 140,455,073 (GRCm39)	F621L	probably damaging	Het
Pde8b	C	A	13: 95,223,347 (GRCm39)	M197I	possibly damaging	Het
Pear1	T	A	3: 87,659,522 (GRCm39)	I771L	probably benign	Het
Poli	A	G	18: 70,655,891 (GRCm39)	L281P	probably damaging	Het
Prdm12	T	C	2: 31,530,231 (GRCm39)	W41R	probably damaging	Het
Prkdc	T	G	16: 15,532,870 (GRCm39)	S1500A	probably benign	Het
Prune2	T	A	19: 17,096,798 (GRCm39)	H767Q	probably benign	Het
Rasgef1b	G	A	5: 99,382,403 (GRCm39)	Q196*	probably null	Het
Rnpc3	A	T	3: 113,416,096 (GRCm39)	L121*	probably null	Het
Rpp14	A	G	14: 8,083,724 (GRCm38)	M1V	probably null	Het
Ryr2	T	A	13: 11,610,610 (GRCm39)	D4072V	probably damaging	Het
Sgms1	T	C	19: 32,102,765 (GRCm39)	H314R	probably damaging	Het
Six4	CT	C	12: 73,151,013 (GRCm39)		probably benign	Het
Slc37a3	A	T	6: 39,324,244 (GRCm39)	Y335N	probably damaging	Het
Tcp11l1	A	T	2: 104,536,837 (GRCm39)	H9Q	probably benign	Het
Tnrc6a	T	A	7: 122,779,057 (GRCm39)	M1256K	probably damaging	Het
Trpc6	A	G	9: 8,609,910 (GRCm39)	N126S	probably damaging	Het
Tut4	T	G	4: 108,374,715 (GRCm39)	C933G	probably damaging	Het
Ubr4	T	C	4: 139,120,373 (GRCm39)	F266S	possibly damaging	Het
Uimc1	A	G	13: 55,217,550 (GRCm39)	V424A	possibly damaging	Het
Utrn	T	C	10: 12,573,873 (GRCm39)	I1066V	probably benign	Het
Vmn1r204	A	G	13: 22,740,404 (GRCm39)	T12A	probably benign	Het
Vmn1r57	T	A	7: 5,223,613 (GRCm39)	I46N	possibly damaging	Het
Vmn1r91	T	C	7: 19,835,839 (GRCm39)	Y253H	probably benign	Het
Vmn2r14	T	A	5: 109,369,219 (GRCm39)	H118L	probably benign	Het
Zfp775	A	G	6: 48,597,404 (GRCm39)	K426R	probably benign	Het

Other mutations in Clcn2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00843:Clcn2	APN	16	20,522,391 (GRCm39)	missense	probably benign	0.08
IGL01657:Clcn2	APN	16	20,532,369 (GRCm39)	missense	probably damaging	1.00
IGL01797:Clcn2	APN	16	20,531,511 (GRCm39)	missense	probably damaging	1.00
IGL02557:Clcn2	APN	16	20,527,214 (GRCm39)	missense	probably damaging	1.00
IGL02624:Clcn2	APN	16	20,522,098 (GRCm39)	missense	probably damaging	0.98
IGL02819:Clcn2	APN	16	20,528,006 (GRCm39)	nonsense	probably null
IGL03329:Clcn2	APN	16	20,530,902 (GRCm39)	missense	probably damaging	1.00
Bemr14	UTSW	16	0 ()	unclassified
R0008:Clcn2	UTSW	16	20,529,140 (GRCm39)	missense	probably null	1.00
R0454:Clcn2	UTSW	16	20,529,178 (GRCm39)	critical splice acceptor site	probably null
R1101:Clcn2	UTSW	16	20,522,345 (GRCm39)	missense	probably damaging	1.00
R1466:Clcn2	UTSW	16	20,531,302 (GRCm39)	splice site	probably benign
R1824:Clcn2	UTSW	16	20,534,712 (GRCm39)	missense	probably benign	0.04
R4592:Clcn2	UTSW	16	20,527,892 (GRCm39)	missense	probably damaging	0.99
R5011:Clcn2	UTSW	16	20,525,965 (GRCm39)	missense	probably damaging	1.00
R5013:Clcn2	UTSW	16	20,525,965 (GRCm39)	missense	probably damaging	1.00
R5154:Clcn2	UTSW	16	20,522,053 (GRCm39)	missense	probably benign	0.01
R5374:Clcn2	UTSW	16	20,528,419 (GRCm39)	missense	possibly damaging	0.78
R5726:Clcn2	UTSW	16	20,529,285 (GRCm39)	intron	probably benign
R5787:Clcn2	UTSW	16	20,522,183 (GRCm39)	missense	probably damaging	1.00
R5992:Clcn2	UTSW	16	20,532,404 (GRCm39)	missense	possibly damaging	0.68
R6045:Clcn2	UTSW	16	20,530,438 (GRCm39)	critical splice donor site	probably null
R6663:Clcn2	UTSW	16	20,521,995 (GRCm39)	makesense	probably null
R6765:Clcn2	UTSW	16	20,526,418 (GRCm39)	splice site	probably null
R6825:Clcn2	UTSW	16	20,528,408 (GRCm39)	utr 3 prime	probably benign
R8028:Clcn2	UTSW	16	20,527,512 (GRCm39)	missense	possibly damaging	0.66
R8198:Clcn2	UTSW	16	20,525,946 (GRCm39)	missense	probably damaging	0.99
R8805:Clcn2	UTSW	16	20,532,168 (GRCm39)	missense	probably damaging	1.00
R8924:Clcn2	UTSW	16	20,530,930 (GRCm39)	missense	probably damaging	1.00
R8992:Clcn2	UTSW	16	20,531,080 (GRCm39)	missense	probably damaging	1.00
R9074:Clcn2	UTSW	16	20,531,414 (GRCm39)	missense	possibly damaging	0.78
R9101:Clcn2	UTSW	16	20,525,979 (GRCm39)	missense	probably benign	0.00
R9456:Clcn2	UTSW	16	20,534,702 (GRCm39)	small deletion	probably benign

Predicted Primers

PCR Primer
(F):5'- GCTACAGGCTGACACTTTAGG -3'
(R):5'- AGTGGAGTCTCCTGGTAAGG -3'

Sequencing Primer
(F):5'- CTACAGGCTGACACTTTAGGAGAATG -3'
(R):5'- TAAGGCCAGGAGGGGTCC -3'

Posted On

2019-12-20