Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02605:Kdm1a'

300251

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Kdm1a

Ensembl Gene

ENSMUSG00000036940

Gene Name

lysine (K)-specific demethylase 1A

Synonyms

Aof2, 1810043O07Rik, Kdm1, LSD1

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL02605

Quality Score

Status

Chromosome

Chromosomal Location

136550540-136602723 bp(-) (GRCm38)

Type of Mutation

unclassified

DNA Base Change (assembly)

G to T at 136551037 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000130758 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001116] [ENSMUST00000063021] [ENSMUST00000105847] [ENSMUST00000105849] [ENSMUST00000116273] [ENSMUST00000168936] [ENSMUST00000170102]

AlphaFold

Q6ZQ88

Predicted Effect

probably benign
Transcript: ENSMUST00000001116

SMART Domains

Protein: ENSMUSP00000001116
Gene: ENSMUSG00000001089

Domain	Start	End	E-Value	Type
SCOP:d1fxkc_	96	233	4e-3	SMART
coiled coil region	264	350	N/A	INTRINSIC
internal_repeat_1	569	638	9.92e-6	PROSPERO
low complexity region	756	769	N/A	INTRINSIC
low complexity region	783	796	N/A	INTRINSIC
internal_repeat_1	986	1056	9.92e-6	PROSPERO

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

probably benign
Transcript: ENSMUST00000063021

SMART Domains

Protein: ENSMUSP00000060619
Gene: ENSMUSG00000001089

Domain	Start	End	E-Value	Type
SCOP:d1fxkc_	96	233	4e-3	SMART
coiled coil region	264	350	N/A	INTRINSIC
internal_repeat_1	569	638	9.92e-6	PROSPERO
low complexity region	756	769	N/A	INTRINSIC
low complexity region	783	796	N/A	INTRINSIC
internal_repeat_1	986	1056	9.92e-6	PROSPERO

Predicted Effect

probably benign
Transcript: ENSMUST00000105847

SMART Domains

Protein: ENSMUSP00000101473
Gene: ENSMUSG00000036940

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

probably benign
Transcript: ENSMUST00000105849

SMART Domains

Protein: ENSMUSP00000101475
Gene: ENSMUSG00000001089

Domain	Start	End	E-Value	Type
SCOP:d1fxkc_	96	233	4e-3	SMART
coiled coil region	264	350	N/A	INTRINSIC
internal_repeat_1	569	638	9.92e-6	PROSPERO
low complexity region	756	769	N/A	INTRINSIC
low complexity region	783	796	N/A	INTRINSIC
internal_repeat_1	986	1056	9.92e-6	PROSPERO

Predicted Effect

probably benign
Transcript: ENSMUST00000116273

SMART Domains

Protein: ENSMUSP00000111977
Gene: ENSMUSG00000036940

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: ENSMUST00000125111

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139690

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147886

Predicted Effect

probably benign
Transcript: ENSMUST00000155354

SMART Domains

Protein: ENSMUSP00000114268
Gene: ENSMUSG00000036940

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

Predicted Effect

probably benign
Transcript: ENSMUST00000168936

Predicted Effect

probably benign
Transcript: ENSMUST00000170102

SMART Domains

Protein: ENSMUSP00000130758
Gene: ENSMUSG00000001089

Domain	Start	End	E-Value	Type
SCOP:d1fxkc_	96	233	4e-3	SMART
coiled coil region	264	350	N/A	INTRINSIC
internal_repeat_1	569	638	9.92e-6	PROSPERO
low complexity region	756	769	N/A	INTRINSIC
low complexity region	783	796	N/A	INTRINSIC
internal_repeat_1	986	1056	9.92e-6	PROSPERO

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000171424

Coding Region Coverage

Validation Efficiency

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
Abtb2	A	T	2: 103,717,257	Y992F	probably benign	Het
Adgrg6	T	A	10: 14,467,232	N324Y	probably damaging	Het
Ampd3	T	C	7: 110,795,758	F305L	probably benign	Het
Ankrd35	A	G	3: 96,681,072		probably null	Het
Api5	A	G	2: 94,429,719	I64T	possibly damaging	Het
Arhgap21	A	G	2: 20,855,588	I1165T	probably damaging	Het
Bdp1	T	C	13: 100,078,115		probably null	Het
Capn3	T	A	2: 120,496,037	I570N	probably damaging	Het
Catsperg2	T	C	7: 29,719,565	H232R	possibly damaging	Het
Clcn7	T	C	17: 25,146,818	L156P	possibly damaging	Het
Cpa3	C	A	3: 20,222,212	V286F	probably benign	Het
Csrnp3	G	A	2: 66,022,809	C527Y	probably damaging	Het
Dock5	A	T	14: 67,828,438	V372E	probably benign	Het
Elmo1	T	C	13: 20,605,202	L696P	probably damaging	Het
Fam91a1	T	C	15: 58,431,196		probably benign	Het
Gm12695	T	A	4: 96,762,751	D155V	probably null	Het
Hspa4l	A	G	3: 40,781,623	I559V	probably benign	Het
Lrrc8d	A	T	5: 105,826,817		noncoding transcript	Het
Minpp1	A	T	19: 32,498,415	Y316F	possibly damaging	Het
Neto2	T	C	8: 85,663,435		probably benign	Het
Nrxn2	T	A	19: 6,450,580	D277E	probably benign	Het
Ola1	A	G	2: 73,142,300		probably benign	Het
Olfr1298	A	G	2: 111,645,505	V164A	probably benign	Het
Olfr550	T	C	7: 102,579,395	I300T	probably damaging	Het
Olfr893	T	A	9: 38,209,236	M61K	probably damaging	Het
Pam	A	G	1: 97,840,339	V722A	possibly damaging	Het
Pfdn6	T	C	17: 33,939,103	Y90C	probably benign	Het
Pkhd1	T	A	1: 20,550,902	H844L	possibly damaging	Het
Plk5	G	A	10: 80,363,062	V422M	probably damaging	Het
Psmc1	G	T	12: 100,119,127	R249L	probably damaging	Het
Ptpro	C	T	6: 137,380,318	P269L	probably benign	Het
Ralgapa1	G	T	12: 55,712,665	H1480Q	possibly damaging	Het
Rars	G	A	11: 35,824,526		probably benign	Het
Rbm48	G	A	5: 3,590,600	R260C	possibly damaging	Het
Smarcc1	C	T	9: 110,222,000	H963Y	possibly damaging	Het
Spef2	T	C	15: 9,725,152	E230G	probably damaging	Het
Spg11	A	G	2: 122,092,260	S903P	probably benign	Het
Tas2r122	T	C	6: 132,711,609	Y107C	probably damaging	Het
Tpm3	C	A	3: 90,088,446	N204K	probably benign	Het
Wdr36	T	C	18: 32,851,991	I450T	possibly damaging	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
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
R3625:Kdm1a	UTSW	4	136561108	missense	possibly damaging	0.93
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

Posted On

2015-04-16