Mutagenetix > Incidental Mutation

Incidental Mutation 'R4850:Kcnt1'

373442

Institutional Source

Beutler Lab

Gene Symbol

Kcnt1

Ensembl Gene

ENSMUSG00000058740

Gene Name

potassium channel, subfamily T, member 1

Synonyms

C030030G16Rik, Slack, slo2

MMRRC Submission

042462-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.230) question?

Stock #

R4850 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

25863734-25918273 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 25908100 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 874 (F874L)

Ref Sequence

ENSEMBL: ENSMUSP00000143482 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000037580] [ENSMUST00000114172] [ENSMUST00000114176] [ENSMUST00000128502] [ENSMUST00000153001] [ENSMUST00000171268] [ENSMUST00000197917] [ENSMUST00000198204] [ENSMUST00000200434]

AlphaFold

Q6ZPR4

Predicted Effect

probably damaging
Transcript: ENSMUST00000037580
AA Change: F910L

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000039058
Gene: ENSMUSG00000058740
AA Change: F910L

Domain	Start	End	E-Value	Type
low complexity region	13	32	N/A	INTRINSIC
transmembrane domain	98	117	N/A	INTRINSIC
transmembrane domain	157	179	N/A	INTRINSIC
transmembrane domain	188	210	N/A	INTRINSIC
Pfam:Ion_trans_2	252	335	1.3e-12	PFAM
transmembrane domain	355	377	N/A	INTRINSIC
Pfam:BK_channel_a	477	579	5.8e-32	PFAM
PDB:3U6N\|H	794	983	6e-6	PDB
low complexity region	1059	1076	N/A	INTRINSIC
low complexity region	1212	1229	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000114172
AA Change: F896L

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

SMART Domains

Protein: ENSMUSP00000109809
Gene: ENSMUSG00000058740
AA Change: F896L

Domain	Start	End	E-Value	Type
low complexity region	13	32	N/A	INTRINSIC
transmembrane domain	98	117	N/A	INTRINSIC
transmembrane domain	157	179	N/A	INTRINSIC
transmembrane domain	188	210	N/A	INTRINSIC
Pfam:Ion_trans_2	255	335	5.2e-13	PFAM
transmembrane domain	355	377	N/A	INTRINSIC
Pfam:BK_channel_a	475	580	3.3e-38	PFAM
PDB:3U6N\|H	792	981	7e-6	PDB
low complexity region	1057	1074	N/A	INTRINSIC
low complexity region	1210	1227	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000114176
AA Change: F910L

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000109813
Gene: ENSMUSG00000058740
AA Change: F910L

Domain	Start	End	E-Value	Type
low complexity region	13	32	N/A	INTRINSIC
transmembrane domain	98	117	N/A	INTRINSIC
transmembrane domain	157	179	N/A	INTRINSIC
transmembrane domain	188	210	N/A	INTRINSIC
Pfam:Ion_trans_2	255	335	5.1e-13	PFAM
transmembrane domain	355	377	N/A	INTRINSIC
Pfam:BK_channel_a	475	580	3.2e-38	PFAM
PDB:3U6N\|H	794	983	6e-6	PDB
low complexity region	1059	1076	N/A	INTRINSIC
low complexity region	1191	1208	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000128502

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131529

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138568

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145544

Predicted Effect

probably damaging
Transcript: ENSMUST00000153001
AA Change: F218L

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000142532
Gene: ENSMUSG00000058740
AA Change: F218L

Domain	Start	End	E-Value	Type
PDB:4HPF\|B	79	285	6e-9	PDB

Predicted Effect

probably damaging
Transcript: ENSMUST00000171268
AA Change: F890L

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000132212
Gene: ENSMUSG00000058740
AA Change: F890L

Domain	Start	End	E-Value	Type
transmembrane domain	78	97	N/A	INTRINSIC
transmembrane domain	137	159	N/A	INTRINSIC
transmembrane domain	168	190	N/A	INTRINSIC
Pfam:Ion_trans_2	235	315	5.1e-13	PFAM
transmembrane domain	335	357	N/A	INTRINSIC
Pfam:BK_channel_a	455	560	3.2e-38	PFAM
PDB:3U6N\|H	774	963	7e-6	PDB
low complexity region	1039	1056	N/A	INTRINSIC
low complexity region	1192	1209	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000197917
AA Change: F908L

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

SMART Domains

Protein: ENSMUSP00000143106
Gene: ENSMUSG00000058740
AA Change: F908L

Domain	Start	End	E-Value	Type
low complexity region	13	32	N/A	INTRINSIC
transmembrane domain	98	117	N/A	INTRINSIC
transmembrane domain	157	179	N/A	INTRINSIC
transmembrane domain	188	210	N/A	INTRINSIC
Pfam:Ion_trans_2	255	335	5.2e-13	PFAM
transmembrane domain	355	377	N/A	INTRINSIC
Pfam:BK_channel_a	475	580	3.3e-38	PFAM
PDB:3U6N\|H	792	981	7e-6	PDB
low complexity region	1057	1074	N/A	INTRINSIC
low complexity region	1210	1227	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000198204
AA Change: F876L

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000142870
Gene: ENSMUSG00000058740
AA Change: F876L

Domain	Start	End	E-Value	Type
transmembrane domain	64	83	N/A	INTRINSIC
transmembrane domain	123	145	N/A	INTRINSIC
transmembrane domain	154	176	N/A	INTRINSIC
Pfam:Ion_trans_2	221	301	5e-11	PFAM
transmembrane domain	321	343	N/A	INTRINSIC
Pfam:BK_channel_a	441	546	1.2e-35	PFAM
PDB:3U6N\|H	760	949	6e-6	PDB
low complexity region	1025	1042	N/A	INTRINSIC
low complexity region	1157	1174	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199269

Predicted Effect

probably damaging
Transcript: ENSMUST00000200434
AA Change: F874L

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

SMART Domains

Protein: ENSMUSP00000143482
Gene: ENSMUSG00000058740
AA Change: F874L

Domain	Start	End	E-Value	Type
transmembrane domain	64	83	N/A	INTRINSIC
transmembrane domain	123	145	N/A	INTRINSIC
transmembrane domain	154	176	N/A	INTRINSIC
Pfam:Ion_trans_2	221	301	5.1e-11	PFAM
transmembrane domain	321	343	N/A	INTRINSIC
Pfam:BK_channel_a	441	546	1.3e-35	PFAM
PDB:3U6N\|H	758	947	6e-6	PDB
low complexity region	1023	1040	N/A	INTRINSIC
low complexity region	1176	1193	N/A	INTRINSIC

Meta Mutation Damage Score

0.5269

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.8%

Validation Efficiency

99% (79/80)

MGI Phenotype

FUNCTION: This gene encodes a member of the Slo potassium channel family that has shown to be activated by both sodium and chloride ions. This channel represents the largest potassium channel subunit yet identified. This channel may be important in development and pain signaling. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired action potential firing in sensory neurons and increased mechanical hypersensitivity in neuropathic pain models. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410089E03Rik	T	C	15: 8,262,938	S3012P	unknown	Het
Abcb10	C	T	8: 123,982,690	A42T	probably benign	Het
Acsf3	T	C	8: 122,817,436	V551A	probably damaging	Het
Adgrl2	G	A	3: 148,859,020	T304I	probably damaging	Het
Akr1d1	A	G	6: 37,554,587		probably null	Het
Ankrd17	A	T	5: 90,264,786	H1226Q	probably damaging	Het
Arap1	T	C	7: 101,398,791	I847T	probably damaging	Het
Atad2b	G	A	12: 4,943,251	G257S	probably benign	Het
Cand2	A	T	6: 115,801,948	T1158S	probably benign	Het
Cic	G	A	7: 25,272,902	R686H	probably damaging	Het
Cldn1	T	A	16: 26,363,163	T99S	probably benign	Het
Cnga3	G	T	1: 37,258,006	E173*	probably null	Het
Cryge	G	T	1: 65,051,052		probably benign	Het
Dsp	T	A	13: 38,192,469	L1410H	probably damaging	Het
Dync2h1	T	C	9: 7,134,364	T1548A	probably benign	Het
Dysf	C	A	6: 84,097,715	D499E	probably damaging	Het
Eml5	T	C	12: 98,790,619	D1917G	probably damaging	Het
Fabp3	C	T	4: 130,312,387	T57I	probably benign	Het
Fam71d	A	G	12: 78,715,153	D197G	probably damaging	Het
Fn3krp	A	T	11: 121,425,053	H90L	possibly damaging	Het
Gm10718	A	T	9: 3,023,716	T56S	probably benign	Het
Gm4847	A	T	1: 166,642,339	I55K	probably damaging	Het
Gsn	T	A	2: 35,283,900		probably null	Het
Haghl	T	C	17: 25,783,006		probably benign	Het
Hist1h2bj	G	T	13: 22,043,251		probably benign	Het
Hmg20b	T	A	10: 81,346,927	E139V	probably damaging	Het
Hsd3b6	G	A	3: 98,807,905	T57I	probably benign	Het
Igkv5-48	A	G	6: 69,726,796	S42P	probably damaging	Het
Igsf23	T	C	7: 19,953,934		probably benign	Het
Maf1	T	C	15: 76,352,962	F110L	possibly damaging	Het
Mtpap	C	T	18: 4,387,044	R365W	probably damaging	Het
Mtus1	A	C	8: 41,084,470	S70A	possibly damaging	Het
Nfatc1	T	A	18: 80,697,865	T307S	probably benign	Het
Nphs1	T	G	7: 30,463,232	S379A	possibly damaging	Het
Nup205	A	G	6: 35,230,530	T1506A	probably benign	Het
Olfr1044	T	A	2: 86,171,671	I49F	probably damaging	Het
Olfr275	T	C	4: 52,825,450	S18P	possibly damaging	Het
Pcdhga8	A	T	18: 37,727,709	Y606F	probably damaging	Het
Pde7a	A	G	3: 19,243,117	V123A	probably benign	Het
Pex1	C	T	5: 3,624,426	T809I	probably benign	Het
Prdm13	C	A	4: 21,678,243	R749L	possibly damaging	Het
Prkcd	A	G	14: 30,599,743	L498P	probably damaging	Het
Pros1	A	T	16: 62,885,524	E67V	probably damaging	Het
Rab44	A	G	17: 29,140,089	E417G	possibly damaging	Het
Rangrf	A	G	11: 68,973,640		probably null	Het
Rp1	T	A	1: 4,348,675	K738M	probably damaging	Het
Ryr2	A	T	13: 11,668,820	D3119E	probably damaging	Het
Ryr2	G	A	13: 11,745,752	R1482C	probably damaging	Het
Sbspon	T	A	1: 15,858,968	T200S	probably damaging	Het
Sfxn5	T	C	6: 85,332,376		probably benign	Het
Slc26a8	T	A	17: 28,654,883	I377F	probably benign	Het
Slc30a7	A	G	3: 115,993,008	F72L	probably damaging	Het
Slc32a1	T	C	2: 158,614,192	F256L	possibly damaging	Het
Slco6b1	T	C	1: 96,911,833		noncoding transcript	Het
Smpd1	A	G	7: 105,555,985	H357R	probably benign	Het
Sncaip	A	T	18: 52,871,384	H361L	probably damaging	Het
Tenm2	A	C	11: 36,023,488	Y2406*	probably null	Het
Terb1	T	A	8: 104,485,425	H308L	probably benign	Het
Trim61	A	T	8: 65,013,418	L397H	probably damaging	Het
Trp53bp1	T	A	2: 121,205,113		probably null	Het
Ttn	T	G	2: 76,781,555	E9007D	possibly damaging	Het
Urb1	A	T	16: 90,795,414	C319*	probably null	Het
Vmn2r95	T	C	17: 18,451,653	Y551H	probably damaging	Het
Vwde	A	T	6: 13,196,048	V326D	possibly damaging	Het
Xdh	A	G	17: 73,898,335	L1045P	probably damaging	Het
Zfp638	T	C	6: 83,979,475	I1688T	possibly damaging	Het
Zwint	T	A	10: 72,655,956		probably benign	Het

Other mutations in Kcnt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00718:Kcnt1	APN	2	25892407	missense	probably damaging	0.98
IGL01358:Kcnt1	APN	2	25916005	missense	probably damaging	1.00
IGL01593:Kcnt1	APN	2	25898754	missense	probably damaging	1.00
IGL01779:Kcnt1	APN	2	25900967	missense	probably damaging	1.00
IGL01800:Kcnt1	APN	2	25888125	missense	probably damaging	1.00
IGL01834:Kcnt1	APN	2	25912719	critical splice donor site	probably null
IGL02001:Kcnt1	APN	2	25908152	missense	probably damaging	1.00
IGL02061:Kcnt1	APN	2	25900482	critical splice donor site	probably null
IGL02121:Kcnt1	APN	2	25901865	missense	probably damaging	1.00
IGL02646:Kcnt1	APN	2	25900880	splice site	probably benign
IGL02683:Kcnt1	APN	2	25900925	missense	possibly damaging	0.85
IGL03028:Kcnt1	APN	2	25909203	critical splice acceptor site	probably null
IGL03139:Kcnt1	APN	2	25894468	splice site	probably benign
R0070:Kcnt1	UTSW	2	25892362	missense	probably benign	0.00
R0070:Kcnt1	UTSW	2	25892362	missense	probably benign	0.00
R0149:Kcnt1	UTSW	2	25898264	splice site	probably benign
R0294:Kcnt1	UTSW	2	25888110	missense	probably damaging	0.99
R0367:Kcnt1	UTSW	2	25907628	missense	probably damaging	1.00
R0481:Kcnt1	UTSW	2	25892496	missense	probably damaging	0.98
R0666:Kcnt1	UTSW	2	25891243	splice site	probably benign
R1364:Kcnt1	UTSW	2	25908094	missense	probably damaging	0.99
R1553:Kcnt1	UTSW	2	25900385	missense	probably damaging	1.00
R1916:Kcnt1	UTSW	2	25900469	missense	probably damaging	1.00
R1999:Kcnt1	UTSW	2	25892360	missense	probably benign
R2079:Kcnt1	UTSW	2	25900248	missense	possibly damaging	0.48
R2166:Kcnt1	UTSW	2	25891183	splice site	probably benign
R2295:Kcnt1	UTSW	2	25900921	missense	probably damaging	1.00
R3688:Kcnt1	UTSW	2	25894359	missense	probably damaging	1.00
R3820:Kcnt1	UTSW	2	25900892	missense	probably damaging	1.00
R3826:Kcnt1	UTSW	2	25915868	critical splice donor site	probably null
R3980:Kcnt1	UTSW	2	25893214	missense	possibly damaging	0.91
R4031:Kcnt1	UTSW	2	25916048	missense	possibly damaging	0.77
R4093:Kcnt1	UTSW	2	25877915	missense	probably damaging	0.99
R4361:Kcnt1	UTSW	2	25878032	missense	probably benign	0.03
R4367:Kcnt1	UTSW	2	25907626	missense	probably damaging	1.00
R5005:Kcnt1	UTSW	2	25901346	missense	probably damaging	1.00
R5119:Kcnt1	UTSW	2	25909322	intron	probably benign
R5223:Kcnt1	UTSW	2	25903422	missense	probably benign
R5243:Kcnt1	UTSW	2	25908074	missense	probably damaging	1.00
R5323:Kcnt1	UTSW	2	25909277	missense	possibly damaging	0.59
R5665:Kcnt1	UTSW	2	25901909	nonsense	probably null
R5888:Kcnt1	UTSW	2	25908110	missense	probably damaging	1.00
R5906:Kcnt1	UTSW	2	25894524	intron	probably benign
R5906:Kcnt1	UTSW	2	25898401	missense	probably damaging	1.00
R5927:Kcnt1	UTSW	2	25909376	intron	probably benign
R6160:Kcnt1	UTSW	2	25892383	missense	probably damaging	0.96
R6161:Kcnt1	UTSW	2	25903385	missense	probably benign	0.00
R6179:Kcnt1	UTSW	2	25893180	missense	probably damaging	1.00
R6222:Kcnt1	UTSW	2	25892510	missense	probably damaging	1.00
R6268:Kcnt1	UTSW	2	25903597	splice site	probably null
R6336:Kcnt1	UTSW	2	25888755	splice site	probably null
R6395:Kcnt1	UTSW	2	25909239	missense	possibly damaging	0.81
R6564:Kcnt1	UTSW	2	25911051	missense	probably benign	0.09
R6944:Kcnt1	UTSW	2	25877828	intron	probably benign
R7236:Kcnt1	UTSW	2	25909939	splice site	probably null
R7308:Kcnt1	UTSW	2	25900463	missense	possibly damaging	0.74
R7346:Kcnt1	UTSW	2	25863843	unclassified	probably benign
R7419:Kcnt1	UTSW	2	25915999	missense	probably benign	0.11
R7461:Kcnt1	UTSW	2	25901346	missense	probably benign	0.01
R7470:Kcnt1	UTSW	2	25909833	missense	probably damaging	0.96
R7566:Kcnt1	UTSW	2	25916036	missense	probably benign	0.31
R7613:Kcnt1	UTSW	2	25901346	missense	probably benign	0.01
R7778:Kcnt1	UTSW	2	25901889	missense	probably benign	0.10
R8031:Kcnt1	UTSW	2	25908042	splice site	probably benign
R8088:Kcnt1	UTSW	2	25894314	missense	possibly damaging	0.63
R8113:Kcnt1	UTSW	2	25901211	missense	possibly damaging	0.67
R8378:Kcnt1	UTSW	2	25907271	missense	probably benign	0.03
R8954:Kcnt1	UTSW	2	25894326	missense	probably benign
R9231:Kcnt1	UTSW	2	25911062	missense	probably benign	0.00
R9445:Kcnt1	UTSW	2	25877947	missense	probably damaging	1.00
R9733:Kcnt1	UTSW	2	25907339	missense	probably benign	0.00
Z1176:Kcnt1	UTSW	2	25906796	missense	probably benign	0.07
Z1177:Kcnt1	UTSW	2	25901228	nonsense	probably null
Z1177:Kcnt1	UTSW	2	25909265	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- AGTTATGACCACAGGATCCACC -3'
(R):5'- ATCTGTTAGCAGTTCCTGGCG -3'

Sequencing Primer
(F):5'- TTATGACCACAGGATCCACCATAGAC -3'
(R):5'- TTAGCAGTTCCTGGCGGATCC -3'

Posted On

2016-03-01