Mutagenetix > Incidental Mutation

Incidental Mutation 'R3625:Kdm1a'

269369

Institutional Source

Beutler Lab

Gene Symbol

Kdm1a

Ensembl Gene

ENSMUSG00000036940

Gene Name

lysine (K)-specific demethylase 1A

Synonyms

Aof2, 1810043O07Rik, Kdm1, LSD1

MMRRC Submission

040679-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3625 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

136550540-136602723 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 136561108 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 388 (E388G)

Ref Sequence

ENSEMBL: ENSMUSP00000111977 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000105847] [ENSMUST00000116273]

AlphaFold

Q6ZQ88

Predicted Effect

probably benign
Transcript: ENSMUST00000046846

SMART Domains

Protein: ENSMUSP00000035457
Gene: ENSMUSG00000036940

Domain	Start	End	E-Value	Type
low complexity region	47	80	N/A	INTRINSIC
Pfam:SWIRM	85	173	1.1e-20	PFAM
Pfam:AlaDh_PNT_C	181	297	8.4e-8	PFAM
Pfam:FAD_binding_2	189	236	1.6e-6	PFAM
Pfam:Pyr_redox	189	237	6.5e-7	PFAM
Pfam:DAO	189	457	1.5e-9	PFAM
Pfam:NAD_binding_8	192	256	9e-16	PFAM
Pfam:Amino_oxidase	197	657	7e-133	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000105847
AA Change: E408G

PolyPhen 2 Score 0.788 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000101473
Gene: ENSMUSG00000036940
AA Change: E408G

Domain	Start	End	E-Value	Type
low complexity region	7	40	N/A	INTRINSIC
low complexity region	76	97	N/A	INTRINSIC
low complexity region	139	172	N/A	INTRINSIC
low complexity region	177	194	N/A	INTRINSIC
Pfam:SWIRM	197	285	8.8e-21	PFAM
Pfam:FAD_binding_2	301	348	6e-6	PFAM
Pfam:Pyr_redox	301	349	3e-6	PFAM
Pfam:DAO	301	557	9.9e-9	PFAM
Pfam:NAD_binding_8	304	368	4e-15	PFAM
Pfam:Amino_oxidase	309	847	2e-133	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000116273
AA Change: E388G

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000111977
Gene: ENSMUSG00000036940
AA Change: E388G

Domain	Start	End	E-Value	Type
low complexity region	7	40	N/A	INTRINSIC
low complexity region	76	97	N/A	INTRINSIC
low complexity region	139	172	N/A	INTRINSIC
Pfam:SWIRM	175	265	2.7e-21	PFAM
Pfam:Pyr_redox	281	327	5.5e-7	PFAM
Pfam:FAD_binding_2	281	328	5.3e-6	PFAM
Pfam:DAO	281	403	3.7e-8	PFAM
Pfam:NAD_binding_8	284	348	5.7e-16	PFAM
Pfam:Amino_oxidase	289	827	9.6e-166	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147886

Predicted Effect

unknown
Transcript: ENSMUST00000155354
AA Change: E29G

SMART Domains

Protein: ENSMUSP00000114268
Gene: ENSMUSG00000036940
AA Change: E29G

Domain	Start	End	E-Value	Type
Pfam:Amino_oxidase	3	250	2.9e-12	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000170979
AA Change: E203G

SMART Domains

Protein: ENSMUSP00000131385
Gene: ENSMUSG00000036940
AA Change: E203G

Domain	Start	End	E-Value	Type
Pfam:SWIRM	1	77	2.5e-18	PFAM
Pfam:Pyr_redox_2	70	142	1.1e-7	PFAM
Pfam:AlaDh_PNT_C	85	195	7.8e-8	PFAM
Pfam:FAD_binding_2	93	140	1.7e-6	PFAM
Pfam:Pyr_redox	93	142	8.2e-7	PFAM
Pfam:DAO	93	319	2.8e-9	PFAM
Pfam:NAD_binding_8	96	160	9.8e-16	PFAM
Pfam:Amino_oxidase	101	313	5.1e-32	PFAM

Meta Mutation Damage Score

0.5820

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.1%

Validation Efficiency

100% (40/40)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a nuclear protein containing a SWIRM domain, a FAD-binding motif, and an amine oxidase domain. This protein is a component of several histone deacetylase complexes, though it silences genes by functioning as a histone demethylase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
PHENOTYPE: Homozygous disruption of this gene results in abnormal gastrulation and early embryonic lethality. Homozygotes lacking the neurospecific isoform are hypoexcitable and display decreased susceptibility to pharmacologically induced seizures. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 40 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Arsi	G	A	18: 60,916,651	G202E	probably benign	Het
Atg3	T	A	16: 45,175,261	I119N	probably benign	Het
Cdh12	G	C	15: 21,358,756	V89L	probably damaging	Het
Cdh3	C	A	8: 106,543,678	H396N	probably damaging	Het
Crygs	C	T	16: 22,805,551	G102D	possibly damaging	Het
Dab2ip	C	A	2: 35,643,891	S43*	probably null	Het
Dmxl2	A	G	9: 54,393,643	S2394P	probably benign	Het
F13a1	T	G	13: 36,898,093	N546H	probably benign	Het
Fbn2	T	C	18: 58,061,742	N1449S	probably damaging	Het
Flywch1	T	C	17: 23,760,201		probably benign	Het
Gm10436	T	C	12: 88,175,961	S296G	probably benign	Het
Gm498	T	C	7: 143,871,854	V80A	possibly damaging	Het
Grxcr2	T	A	18: 41,998,818	D62V	probably damaging	Het
Hist1h2bg	T	C	13: 23,571,451		probably benign	Het
Ifnab	A	T	4: 88,690,779	I150N	probably damaging	Het
Igsf8	T	C	1: 172,317,769	V284A	probably benign	Het
Map3k8	G	A	18: 4,333,965	R376C	probably damaging	Het
Map6	A	T	7: 99,269,195	T189S	possibly damaging	Het
Mms22l	T	A	4: 24,505,357	S206T	probably damaging	Het
N4bp1	A	G	8: 86,851,709	L676S	probably damaging	Het
Nkx6-2	A	G	7: 139,582,190	F117S	possibly damaging	Het
Ociad2	C	T	5: 73,323,830	C72Y	probably damaging	Het
Olfr1490	T	A	19: 13,654,982	C184*	probably null	Het
Olfr672	A	T	7: 104,995,984	F307I	probably benign	Het
Pcdhb6	G	T	18: 37,336,140	V21L	probably damaging	Het
Pogk	G	A	1: 166,403,512	T82I	probably damaging	Het
Prkcsh	A	G	9: 22,011,252	E283G	probably null	Het
Prkd3	C	T	17: 78,985,304	R113H	probably damaging	Het
Rabgef1	T	C	5: 130,212,120		probably null	Het
Rec8	T	C	14: 55,622,497	I234T	possibly damaging	Het
Sim1	A	T	10: 50,981,336	H394L	probably benign	Het
Thy1	A	G	9: 44,046,731	E52G	probably damaging	Het
Trav14n-3	A	T	14: 53,370,086	I4F	probably damaging	Het
Trim15	T	C	17: 36,866,876	T76A	possibly damaging	Het
Ttn	A	G	2: 76,768,801	I19288T	probably damaging	Het
Vmn1r6	C	T	6: 57,002,935	T172I	probably damaging	Het
Vmn2r52	A	T	7: 10,159,178	L678Q	probably damaging	Het
Vpreb1	T	C	16: 16,868,804	H74R	probably benign	Het
Yeats4	T	C	10: 117,220,368	I100V	probably benign	Het
Zfp36	C	A	7: 28,378,256	A76S	probably benign	Het

Other mutations in Kdm1a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00796:Kdm1a	APN	4	136554247	missense	probably damaging	1.00
IGL01106:Kdm1a	APN	4	136572328	splice site	probably benign
IGL01356:Kdm1a	APN	4	136553891	missense	probably damaging	1.00
IGL01886:Kdm1a	APN	4	136561016	critical splice donor site	probably null
IGL02605:Kdm1a	APN	4	136551037	unclassified	probably benign
IGL02885:Kdm1a	APN	4	136552535	missense	probably benign	0.00
Seven_falls	UTSW	4	136568600	nonsense	probably null
R0095:Kdm1a	UTSW	4	136550894	missense	probably benign	0.09
R0532:Kdm1a	UTSW	4	136561066	missense	probably damaging	1.00
R0553:Kdm1a	UTSW	4	136555298	missense	probably damaging	1.00
R4085:Kdm1a	UTSW	4	136551962	nonsense	probably null
R4285:Kdm1a	UTSW	4	136582036	splice site	probably null
R5118:Kdm1a	UTSW	4	136557358	unclassified	probably benign
R5493:Kdm1a	UTSW	4	136557421	frame shift	probably null
R5800:Kdm1a	UTSW	4	136573070	splice site	probably null
R5945:Kdm1a	UTSW	4	136568701	splice site	probably null
R6256:Kdm1a	UTSW	4	136568600	nonsense	probably null
R6508:Kdm1a	UTSW	4	136554310	missense	probably damaging	1.00
R7243:Kdm1a	UTSW	4	136551954	missense	probably damaging	1.00
R7270:Kdm1a	UTSW	4	136552527	missense	probably damaging	0.97
R7723:Kdm1a	UTSW	4	136557749	missense	probably benign	0.06
R8391:Kdm1a	UTSW	4	136553843	missense	probably benign	0.45
R8698:Kdm1a	UTSW	4	136559207	missense	probably benign	0.00
R8840:Kdm1a	UTSW	4	136560405	missense	probably damaging	1.00
R9146:Kdm1a	UTSW	4	136602428	missense	unknown
R9778:Kdm1a	UTSW	4	136552581	missense	probably damaging	0.98
X0066:Kdm1a	UTSW	4	136559225	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- AAAAGTGGCCTTGGGGATTC -3'
(R):5'- CAGGCCTGAAACATTTCATATCTC -3'

Sequencing Primer
(F):5'- CTGTTACTATACAGACAGCCCTTAGG -3'
(R):5'- AGTCAAATCATTGTCCTCAAAGG -3'

Posted On

2015-02-19