Mutagenetix > Incidental Mutation

Incidental Mutation 'R5028:Kif1a'

391485

Institutional Source

Beutler Lab

Gene Symbol

Kif1a

Ensembl Gene

ENSMUSG00000014602

Gene Name

kinesin family member 1A

Synonyms

N-3 kinesin, C630002N23Rik, Kns1, LOC381283, ATSV

MMRRC Submission

042619-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.846) question?

Stock #

R5028 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

92943186-93029673 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 92982049 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 793 (I793F)

Ref Sequence

ENSEMBL: ENSMUSP00000140163 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000086819] [ENSMUST00000112958] [ENSMUST00000171556] [ENSMUST00000171796] [ENSMUST00000190723]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000086819
AA Change: I793F

PolyPhen 2 Score 0.666 (Sensitivity: 0.86; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000084029
Gene: ENSMUSG00000014602
AA Change: I793F

Domain	Start	End	E-Value	Type
KISc	3	362	1.05e-177	SMART
low complexity region	411	429	N/A	INTRINSIC
FHA	524	581	1.39e-8	SMART
coiled coil region	634	688	N/A	INTRINSIC
low complexity region	693	706	N/A	INTRINSIC
low complexity region	762	778	N/A	INTRINSIC
Pfam:KIF1B	814	861	6.4e-13	PFAM
Pfam:DUF3694	1157	1305	1.8e-47	PFAM
low complexity region	1420	1444	N/A	INTRINSIC
low complexity region	1541	1549	N/A	INTRINSIC
PH	1584	1683	1.52e-13	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000112958
AA Change: I784F

PolyPhen 2 Score 0.441 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000108582
Gene: ENSMUSG00000014602
AA Change: I784F

Domain	Start	End	E-Value	Type
KISc	3	362	1.05e-177	SMART
low complexity region	402	420	N/A	INTRINSIC
FHA	515	572	1.39e-8	SMART
coiled coil region	625	679	N/A	INTRINSIC
low complexity region	684	697	N/A	INTRINSIC
low complexity region	753	769	N/A	INTRINSIC
Pfam:KIF1B	805	851	3.9e-15	PFAM
Pfam:DUF3694	1148	1304	5e-40	PFAM
low complexity region	1420	1444	N/A	INTRINSIC
low complexity region	1541	1549	N/A	INTRINSIC
PH	1584	1683	1.52e-13	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000171556
AA Change: I784F

PolyPhen 2 Score 0.260 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000130717
Gene: ENSMUSG00000014602
AA Change: I784F

Domain	Start	End	E-Value	Type
KISc	3	362	1.05e-177	SMART
low complexity region	402	420	N/A	INTRINSIC
FHA	515	572	1.39e-8	SMART
coiled coil region	625	679	N/A	INTRINSIC
low complexity region	684	697	N/A	INTRINSIC
low complexity region	753	769	N/A	INTRINSIC
Pfam:KIF1B	805	852	2.7e-13	PFAM
Pfam:DUF3694	1148	1296	8.4e-48	PFAM
low complexity region	1411	1435	N/A	INTRINSIC
low complexity region	1532	1540	N/A	INTRINSIC
PH	1575	1674	1.52e-13	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000171796
AA Change: I784F

PolyPhen 2 Score 0.260 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000128432
Gene: ENSMUSG00000014602
AA Change: I784F

Domain	Start	End	E-Value	Type
KISc	3	362	1.05e-177	SMART
low complexity region	402	420	N/A	INTRINSIC
FHA	515	572	1.39e-8	SMART
coiled coil region	625	679	N/A	INTRINSIC
low complexity region	684	697	N/A	INTRINSIC
low complexity region	753	769	N/A	INTRINSIC
Pfam:KIF1B	805	852	6.4e-13	PFAM
Pfam:DUF3694	1148	1304	1.8e-46	PFAM
low complexity region	1419	1443	N/A	INTRINSIC
low complexity region	1540	1548	N/A	INTRINSIC
PH	1583	1682	1.52e-13	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000186828

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000188493

Predicted Effect

possibly damaging
Transcript: ENSMUST00000190723
AA Change: I793F

PolyPhen 2 Score 0.676 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000140163
Gene: ENSMUSG00000014602
AA Change: I793F

Domain	Start	End	E-Value	Type
KISc	3	362	5.2e-180	SMART
low complexity region	411	429	N/A	INTRINSIC
coiled coil region	438	471	N/A	INTRINSIC
FHA	524	581	6.9e-11	SMART
coiled coil region	634	688	N/A	INTRINSIC
low complexity region	693	706	N/A	INTRINSIC
low complexity region	762	778	N/A	INTRINSIC
Pfam:KIF1B	814	861	4e-10	PFAM
low complexity region	885	900	N/A	INTRINSIC
coiled coil region	901	929	N/A	INTRINSIC
internal_repeat_1	938	957	5.9e-5	PROSPERO
Pfam:DUF3694	1250	1398	1.1e-44	PFAM
low complexity region	1513	1537	N/A	INTRINSIC
low complexity region	1634	1642	N/A	INTRINSIC
PH	1677	1776	6.9e-16	SMART

Meta Mutation Damage Score

0.1196

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.5%
20x: 93.1%

Validation Efficiency

97% (62/64)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the kinesin family and functions as an anterograde motor protein that transports membranous organelles along axonal microtubules. Mutations at this locus have been associated with spastic paraplegia-30 and hereditary sensory neuropathy IIC. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Apr 2012]
PHENOTYPE: Most mice homozygous for a null allele die within a day of birth, with reduced motor and sensory deficits, decreased synaptic vesicle precursor transport, and significant neuronal degeneration in the central nervous system, but two point mutant alleles cause progressive hindleg paralysis [provided by MGI curators]

Allele List at MGI

All alleles(2) : Targeted, other(1) Gene trapped(1)

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb11	T	A	2: 69,104,356 (GRCm39)	S777C	probably damaging	Het
Ano5	T	A	7: 51,187,458 (GRCm39)		probably null	Het
Arhgap17	T	A	7: 122,893,896 (GRCm39)	H508L	probably benign	Het
Arhgap29	T	A	3: 121,803,709 (GRCm39)		probably null	Het
Atp12a	T	C	14: 56,624,435 (GRCm39)	F961S	probably damaging	Het
B4galnt4	C	A	7: 140,647,975 (GRCm39)	P497Q	probably benign	Het
Camsap1	A	G	2: 25,834,568 (GRCm39)	S364P	probably damaging	Het
Ccdc150	C	A	1: 54,302,636 (GRCm39)	D85E	probably benign	Het
Cdc45	A	G	16: 18,613,930 (GRCm39)	Y291H	probably benign	Het
Comp	A	C	8: 70,829,290 (GRCm39)	N289T	probably damaging	Het
Cops3	T	A	11: 59,708,856 (GRCm39)		probably benign	Het
Crybg1	G	A	10: 43,874,208 (GRCm39)	H967Y	possibly damaging	Het
Csmd1	A	T	8: 16,039,090 (GRCm39)	F2423I	probably damaging	Het
Dact1	C	A	12: 71,365,347 (GRCm39)	C709*	probably null	Het
Dcxr	T	G	11: 120,617,273 (GRCm39)	Q90P	probably damaging	Het
Ell	A	G	8: 71,043,349 (GRCm39)	Y494C	probably damaging	Het
Emilin2	T	C	17: 71,581,727 (GRCm39)	E333G	possibly damaging	Het
Eml2	T	C	7: 18,913,372 (GRCm39)		probably null	Het
Fam186b	T	A	15: 99,178,682 (GRCm39)	M215L	probably damaging	Het
Gm17078	T	A	14: 51,848,699 (GRCm39)	R13W	probably null	Het
Gm4787	G	C	12: 81,424,604 (GRCm39)	T518S	probably benign	Het
Hspa14	A	G	2: 3,499,206 (GRCm39)	F196S	possibly damaging	Het
Ier5	A	G	1: 154,974,849 (GRCm39)	S110P	possibly damaging	Het
Lrrc43	T	C	5: 123,646,176 (GRCm39)	I643T	probably damaging	Het
Map3k19	A	T	1: 127,750,969 (GRCm39)	L794Q	probably benign	Het
Meox2	A	T	12: 37,158,935 (GRCm39)	M36L	probably benign	Het
Mgat5b	T	A	11: 116,875,855 (GRCm39)	L693Q	probably damaging	Het
Mup4	T	A	4: 59,958,124 (GRCm39)	E148V	possibly damaging	Het
Napb	T	C	2: 148,545,057 (GRCm39)	N162S	possibly damaging	Het
Nlgn2	T	C	11: 69,718,563 (GRCm39)	D339G	probably benign	Het
Nucks1	C	T	1: 131,855,840 (GRCm39)	R90C	possibly damaging	Het
Or11g7	T	C	14: 50,691,196 (GRCm39)	V229A	probably damaging	Het
Or5an9	T	A	19: 12,187,518 (GRCm39)	V196E	possibly damaging	Het
Plekhd1	A	T	12: 80,739,723 (GRCm39)	D24V	probably damaging	Het
Prpf4b	C	T	13: 35,083,958 (GRCm39)	P909L	probably damaging	Het
Rasgrp1	T	A	2: 117,132,485 (GRCm39)	K116*	probably null	Het
Ror1	A	G	4: 100,269,133 (GRCm39)	T324A	possibly damaging	Het
Slc24a4	G	A	12: 102,230,629 (GRCm39)	G505R	probably damaging	Het
Slc8a1	A	G	17: 81,956,702 (GRCm39)	I112T	possibly damaging	Het
Smarcc2	A	G	10: 128,297,314 (GRCm39)	S69G	probably damaging	Het
Smc2	A	T	4: 52,458,447 (GRCm39)	E429D	probably damaging	Het
Sry	T	C	Y: 2,663,312 (GRCm39)	D116G	probably damaging	Het
Tcea3	T	A	4: 135,985,246 (GRCm39)	V154E	possibly damaging	Het
Tigd2	G	A	6: 59,188,205 (GRCm39)	W357*	probably null	Het
Tmem177	T	A	1: 119,838,419 (GRCm39)	T87S	probably benign	Het
Treh	A	T	9: 44,594,186 (GRCm39)	E144V	probably null	Het
Trpm6	T	A	19: 18,764,124 (GRCm39)	D243E	probably damaging	Het
Ttn	T	C	2: 76,608,394 (GRCm39)	D17843G	probably damaging	Het
Vars2	A	C	17: 35,970,365 (GRCm39)		probably null	Het
Vmn1r201	G	A	13: 22,659,530 (GRCm39)	W248*	probably null	Het
Yap1	T	C	9: 8,001,690 (GRCm39)	T99A	probably benign	Het
Zbtb8b	C	A	4: 129,326,793 (GRCm39)	C91F	probably damaging	Het
Zfp882	A	G	8: 72,668,498 (GRCm39)	T442A	possibly damaging	Het
Zxdc	G	T	6: 90,359,320 (GRCm39)	G651C	probably benign	Het

Other mutations in Kif1a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00230:Kif1a	APN	1	92,982,656 (GRCm39)	missense	probably damaging	1.00
IGL01574:Kif1a	APN	1	93,010,062 (GRCm39)	missense	probably damaging	1.00
IGL01637:Kif1a	APN	1	92,967,575 (GRCm39)	missense	possibly damaging	0.95
IGL01895:Kif1a	APN	1	92,953,455 (GRCm39)	missense	possibly damaging	0.65
IGL02215:Kif1a	APN	1	92,948,271 (GRCm39)	missense	probably benign	0.05
IGL02571:Kif1a	APN	1	92,948,178 (GRCm39)	critical splice donor site	probably null
IGL02734:Kif1a	APN	1	92,990,280 (GRCm39)	missense	probably damaging	1.00
IGL02752:Kif1a	APN	1	92,967,569 (GRCm39)	missense	possibly damaging	0.92
IGL02990:Kif1a	APN	1	92,966,985 (GRCm39)	missense	probably damaging	1.00
IGL03298:Kif1a	APN	1	92,993,903 (GRCm39)	missense	probably damaging	1.00
IGL03309:Kif1a	APN	1	92,986,579 (GRCm39)	nonsense	probably null
IGL03354:Kif1a	APN	1	92,987,957 (GRCm39)	missense	probably damaging	1.00
asbestos	UTSW	1	92,950,227 (GRCm39)	missense	probably damaging	1.00
chrysolite	UTSW	1	93,002,670 (GRCm39)	splice site	probably benign
osmium	UTSW	1	92,986,532 (GRCm39)	splice site	probably benign
R4538_Kif1a_397	UTSW	1	93,004,769 (GRCm39)	missense	probably damaging	1.00
1mM(1):Kif1a	UTSW	1	93,004,790 (GRCm39)	missense	probably benign	0.00
IGL03046:Kif1a	UTSW	1	93,010,128 (GRCm39)	missense	probably damaging	1.00
PIT4508001:Kif1a	UTSW	1	92,974,451 (GRCm39)	missense	probably damaging	1.00
R0025:Kif1a	UTSW	1	92,970,080 (GRCm39)	missense	probably damaging	1.00
R0115:Kif1a	UTSW	1	92,974,500 (GRCm39)	splice site	probably benign
R0243:Kif1a	UTSW	1	92,969,815 (GRCm39)	missense	probably damaging	1.00
R0270:Kif1a	UTSW	1	92,982,164 (GRCm39)	splice site	probably benign
R0335:Kif1a	UTSW	1	92,980,288 (GRCm39)	splice site	probably benign
R0380:Kif1a	UTSW	1	92,983,753 (GRCm39)	critical splice acceptor site	probably null
R0472:Kif1a	UTSW	1	92,946,719 (GRCm39)	missense	probably damaging	0.99
R0501:Kif1a	UTSW	1	92,983,967 (GRCm39)	missense	probably damaging	1.00
R0538:Kif1a	UTSW	1	92,971,360 (GRCm39)	missense	probably damaging	0.99
R0628:Kif1a	UTSW	1	92,947,605 (GRCm39)	missense	probably damaging	1.00
R0848:Kif1a	UTSW	1	92,947,620 (GRCm39)	missense	probably damaging	1.00
R1110:Kif1a	UTSW	1	92,951,175 (GRCm39)	splice site	probably benign
R1132:Kif1a	UTSW	1	92,983,743 (GRCm39)	missense	probably damaging	0.99
R1387:Kif1a	UTSW	1	92,983,672 (GRCm39)	splice site	probably benign
R1466:Kif1a	UTSW	1	92,982,651 (GRCm39)	missense	possibly damaging	0.68
R1466:Kif1a	UTSW	1	92,982,651 (GRCm39)	missense	possibly damaging	0.68
R1544:Kif1a	UTSW	1	93,002,670 (GRCm39)	splice site	probably benign
R1569:Kif1a	UTSW	1	92,986,532 (GRCm39)	splice site	probably benign
R1802:Kif1a	UTSW	1	92,993,871 (GRCm39)	missense	probably damaging	1.00
R1917:Kif1a	UTSW	1	92,946,753 (GRCm39)	missense	possibly damaging	0.95
R1919:Kif1a	UTSW	1	92,946,753 (GRCm39)	missense	possibly damaging	0.95
R1999:Kif1a	UTSW	1	92,988,517 (GRCm39)	missense	probably damaging	0.98
R2000:Kif1a	UTSW	1	92,982,051 (GRCm39)	missense	probably damaging	0.99
R2276:Kif1a	UTSW	1	92,996,199 (GRCm39)	splice site	probably benign
R2307:Kif1a	UTSW	1	93,006,491 (GRCm39)	missense	probably damaging	1.00
R2919:Kif1a	UTSW	1	92,974,464 (GRCm39)	missense	probably damaging	1.00
R3440:Kif1a	UTSW	1	92,964,575 (GRCm39)	missense	possibly damaging	0.53
R3441:Kif1a	UTSW	1	92,964,575 (GRCm39)	missense	possibly damaging	0.53
R3618:Kif1a	UTSW	1	93,004,765 (GRCm39)	missense	probably null	1.00
R3957:Kif1a	UTSW	1	92,953,416 (GRCm39)	missense	probably damaging	1.00
R4010:Kif1a	UTSW	1	92,950,131 (GRCm39)	missense	probably benign	0.42
R4013:Kif1a	UTSW	1	93,004,014 (GRCm39)	missense	probably damaging	1.00
R4017:Kif1a	UTSW	1	93,004,014 (GRCm39)	missense	probably damaging	1.00
R4115:Kif1a	UTSW	1	92,980,260 (GRCm39)	missense	probably damaging	1.00
R4386:Kif1a	UTSW	1	92,996,272 (GRCm39)	missense	probably damaging	1.00
R4538:Kif1a	UTSW	1	93,004,769 (GRCm39)	missense	probably damaging	1.00
R4608:Kif1a	UTSW	1	92,952,368 (GRCm39)	missense	possibly damaging	0.81
R4625:Kif1a	UTSW	1	92,970,381 (GRCm39)	missense	probably benign	0.00
R4701:Kif1a	UTSW	1	93,006,557 (GRCm39)	missense	probably damaging	0.99
R4794:Kif1a	UTSW	1	92,953,449 (GRCm39)	missense	probably damaging	1.00
R4830:Kif1a	UTSW	1	92,948,931 (GRCm39)	splice site	probably null
R4903:Kif1a	UTSW	1	92,949,456 (GRCm39)	missense	probably damaging	1.00
R4915:Kif1a	UTSW	1	93,002,700 (GRCm39)	missense	probably benign	0.21
R4918:Kif1a	UTSW	1	93,002,700 (GRCm39)	missense	probably benign	0.21
R4991:Kif1a	UTSW	1	93,006,530 (GRCm39)	missense	probably benign	0.00
R5051:Kif1a	UTSW	1	93,003,876 (GRCm39)	splice site	probably null
R5073:Kif1a	UTSW	1	92,950,227 (GRCm39)	missense	probably damaging	1.00
R5103:Kif1a	UTSW	1	92,974,418 (GRCm39)	missense	probably damaging	1.00
R5314:Kif1a	UTSW	1	92,946,220 (GRCm39)	missense	probably damaging	1.00
R5481:Kif1a	UTSW	1	92,987,966 (GRCm39)	missense	probably benign	0.01
R5510:Kif1a	UTSW	1	92,969,414 (GRCm39)	missense	possibly damaging	0.93
R5610:Kif1a	UTSW	1	92,953,450 (GRCm39)	missense	probably damaging	1.00
R5643:Kif1a	UTSW	1	92,983,489 (GRCm39)	missense	probably damaging	0.98
R5808:Kif1a	UTSW	1	92,970,420 (GRCm39)	missense	probably damaging	0.99
R6027:Kif1a	UTSW	1	92,953,365 (GRCm39)	missense	probably benign	0.33
R6056:Kif1a	UTSW	1	92,952,370 (GRCm39)	missense	probably damaging	1.00
R6077:Kif1a	UTSW	1	92,982,618 (GRCm39)	missense	possibly damaging	0.54
R6120:Kif1a	UTSW	1	92,952,296 (GRCm39)	splice site	probably null
R6126:Kif1a	UTSW	1	92,947,621 (GRCm39)	missense	probably damaging	1.00
R6130:Kif1a	UTSW	1	92,964,623 (GRCm39)	missense	probably damaging	1.00
R6255:Kif1a	UTSW	1	92,947,705 (GRCm39)	missense	probably damaging	1.00
R6301:Kif1a	UTSW	1	92,982,663 (GRCm39)	nonsense	probably null
R6326:Kif1a	UTSW	1	93,004,048 (GRCm39)	missense	probably damaging	1.00
R6594:Kif1a	UTSW	1	92,949,035 (GRCm39)	missense	probably benign	0.00
R6653:Kif1a	UTSW	1	93,005,420 (GRCm39)	missense	probably damaging	1.00
R6791:Kif1a	UTSW	1	92,993,859 (GRCm39)	missense	probably damaging	1.00
R6853:Kif1a	UTSW	1	92,967,524 (GRCm39)	missense	possibly damaging	0.47
R7022:Kif1a	UTSW	1	92,993,820 (GRCm39)	missense	probably benign	0.31
R7059:Kif1a	UTSW	1	92,974,551 (GRCm39)	intron	probably benign
R7103:Kif1a	UTSW	1	93,005,507 (GRCm39)	missense	probably damaging	1.00
R7248:Kif1a	UTSW	1	92,969,305 (GRCm39)	missense	probably benign	0.35
R7259:Kif1a	UTSW	1	93,001,532 (GRCm39)	nonsense	probably null
R7424:Kif1a	UTSW	1	92,982,039 (GRCm39)	missense	possibly damaging	0.89
R7659:Kif1a	UTSW	1	92,974,542 (GRCm39)	intron	probably benign
R7681:Kif1a	UTSW	1	92,982,666 (GRCm39)	missense	probably benign
R7976:Kif1a	UTSW	1	92,967,496 (GRCm39)	missense	probably damaging	1.00
R8056:Kif1a	UTSW	1	92,982,423 (GRCm39)	intron	probably benign
R8420:Kif1a	UTSW	1	92,950,141 (GRCm39)	missense	probably benign
R8994:Kif1a	UTSW	1	92,983,457 (GRCm39)	missense	possibly damaging	0.77
R9016:Kif1a	UTSW	1	92,953,395 (GRCm39)	missense	probably damaging	1.00
R9206:Kif1a	UTSW	1	92,979,202 (GRCm39)	missense	probably damaging	0.99
R9246:Kif1a	UTSW	1	93,005,501 (GRCm39)	missense	probably damaging	0.98
R9252:Kif1a	UTSW	1	93,002,776 (GRCm39)	missense	probably damaging	1.00
R9388:Kif1a	UTSW	1	93,000,029 (GRCm39)	critical splice donor site	probably null
R9413:Kif1a	UTSW	1	92,949,019 (GRCm39)	missense	probably benign	0.00
R9612:Kif1a	UTSW	1	92,953,416 (GRCm39)	missense	probably damaging	1.00
R9621:Kif1a	UTSW	1	92,983,445 (GRCm39)	missense	probably benign
R9625:Kif1a	UTSW	1	93,000,766 (GRCm39)	missense	probably benign	0.42
R9694:Kif1a	UTSW	1	92,950,173 (GRCm39)	missense	probably benign
Z1176:Kif1a	UTSW	1	92,950,213 (GRCm39)	missense	probably damaging	1.00
Z1176:Kif1a	UTSW	1	92,949,038 (GRCm39)	missense	probably damaging	0.97
Z1176:Kif1a	UTSW	1	92,983,419 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- TTCAACCAGGAGACACAGTGG -3'
(R):5'- TATGGAATACAGAGCTGAGTTCTCAG -3'

Sequencing Primer
(F):5'- TTCAACCAGGAGACACAGTGGTATTG -3'
(R):5'- AGCTGAGTTCTCAGGGGGATG -3'

Posted On

2016-06-06