Mutagenetix > Incidental Mutation

Incidental Mutation 'R5493:Kdm1a'

432167

Institutional Source

Beutler Lab

Gene Symbol

Kdm1a

Ensembl Gene

ENSMUSG00000036940

Gene Name

lysine (K)-specific demethylase 1A

Synonyms

1810043O07Rik, Kdm1, LSD1, Aof2

MMRRC Submission

043054-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5493 (G1)

Quality Score

120

Status

Validated

Chromosome

Chromosomal Location

136277851-136330034 bp(-) (GRCm39)

Type of Mutation

frame shift

DNA Base Change (assembly)

ACC to AC at 136284732 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Gene Model

predicted gene model for transcript(s): [ENSMUST00000105847] [ENSMUST00000116273] [ENSMUST00000168936]

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

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: 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 null
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

noncoding transcript
Transcript: ENSMUST00000171424

Predicted Effect

probably benign
Transcript: ENSMUST00000168936

Predicted Effect

probably benign
Transcript: ENSMUST00000170979

SMART Domains

Protein: ENSMUSP00000131385
Gene: ENSMUSG00000036940

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

0.9755

Coding Region Coverage

1x: 98.3%
3x: 97.3%
10x: 95.1%
20x: 90.4%

Validation Efficiency

99% (80/81)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510009E07Rik	A	G	16: 21,471,993 (GRCm39)	S236P	possibly damaging	Het
A830018L16Rik	C	T	1: 11,615,431 (GRCm39)	R135C	probably damaging	Het
Agpat3	A	G	10: 78,120,069 (GRCm39)	V155A	possibly damaging	Het
Aldh18a1	C	T	19: 40,539,734 (GRCm39)	R747Q	probably damaging	Het
Aloxe3	A	T	11: 69,019,443 (GRCm39)	R119*	probably null	Het
Asap1	A	G	15: 64,002,000 (GRCm39)	V460A	possibly damaging	Het
Bicral	C	A	17: 47,112,620 (GRCm39)	R860L	possibly damaging	Het
Cd180	T	A	13: 102,842,649 (GRCm39)	I565N	probably benign	Het
Cdk13	T	C	13: 17,978,147 (GRCm39)		probably benign	Het
Cdkn2d	T	C	9: 21,200,303 (GRCm39)	D156G	probably benign	Het
Clrn1	A	G	3: 58,753,837 (GRCm39)	S175P	probably damaging	Het
Coro7	A	G	16: 4,450,351 (GRCm39)	L535S	probably damaging	Het
Cse1l	A	G	2: 166,783,110 (GRCm39)		probably benign	Het
Cyp2a12	T	C	7: 26,728,550 (GRCm39)	L7P	unknown	Het
D130043K22Rik	A	G	13: 25,047,586 (GRCm39)	Y377C	probably damaging	Het
Dctn1	G	T	6: 83,159,546 (GRCm39)	R8L	possibly damaging	Het
Duox2	T	C	2: 122,111,977 (GRCm39)	Q1341R	probably damaging	Het
Eif2b3	A	G	4: 116,943,919 (GRCm39)	D447G	possibly damaging	Het
Eif4a3l1	C	G	6: 136,306,555 (GRCm39)	R339G	probably damaging	Het
Fbxw25	T	C	9: 109,481,984 (GRCm39)	Y234C	probably benign	Het
Gcnt2	A	G	13: 41,107,076 (GRCm39)	N315S	possibly damaging	Het
Gm20730	A	T	6: 43,058,746 (GRCm39)	V22E	possibly damaging	Het
Gm4847	T	A	1: 166,457,890 (GRCm39)	I488F	probably damaging	Het
Gmds	A	T	13: 32,124,488 (GRCm39)	M290K	probably benign	Het
Gtf3c1	T	C	7: 125,269,716 (GRCm39)	N699S	probably damaging	Het
Hk3	A	G	13: 55,158,984 (GRCm39)	V479A	probably damaging	Het
Ifnlr1	G	A	4: 135,432,877 (GRCm39)	V438M	probably benign	Het
Il12rb1	C	A	8: 71,262,483 (GRCm39)	P26T	probably benign	Het
Il4i1	G	T	7: 44,489,477 (GRCm39)	R414L	possibly damaging	Het
Ipo4	T	C	14: 55,868,327 (GRCm39)	N490S	probably benign	Het
Kcnmb2	A	G	3: 32,252,291 (GRCm39)	E164G	probably damaging	Het
Kcns1	G	A	2: 164,009,899 (GRCm39)	L287F	probably benign	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Knl1	T	A	2: 118,899,211 (GRCm39)	I304K	probably damaging	Het
Ksr2	G	T	5: 117,846,175 (GRCm39)	V681F	probably damaging	Het
Lypd2	T	C	15: 74,606,127 (GRCm39)	T4A	probably benign	Het
Man1a	A	G	10: 53,950,576 (GRCm39)	V182A	probably benign	Het
Or12j4	A	T	7: 140,046,720 (GRCm39)	D202V	probably damaging	Het
Or13e8	A	G	4: 43,696,225 (GRCm39)	F316S	possibly damaging	Het
Or2w2	A	T	13: 21,758,042 (GRCm39)	C195S	probably damaging	Het
Or51f5	A	T	7: 102,424,315 (GRCm39)	R195W	probably benign	Het
Or56b1b	T	C	7: 108,164,774 (GRCm39)	D76G	probably benign	Het
Pcdha2	C	A	18: 37,072,562 (GRCm39)	F64L	probably damaging	Het
Pgap3	G	C	11: 98,281,540 (GRCm39)	F168L	possibly damaging	Het
Pip5k1b	T	C	19: 24,416,439 (GRCm39)	N16S	probably benign	Het
Ppip5k1	T	A	2: 121,167,253 (GRCm39)	H41L	probably damaging	Het
Ppp1r9a	A	G	6: 5,159,702 (GRCm39)	R1080G	probably damaging	Het
Qrich2	A	C	11: 116,336,774 (GRCm39)		probably null	Het
Rbl2	C	T	8: 91,842,447 (GRCm39)	P1034L	probably damaging	Het
Rbpjl	GCC	GC	2: 164,256,330 (GRCm39)		probably null	Het
Rin2	A	G	2: 145,702,629 (GRCm39)	S442G	probably damaging	Het
Rtca	C	T	3: 116,293,280 (GRCm39)	R71Q	probably benign	Het
Serpind1	A	T	16: 17,157,902 (GRCm39)	N366I	probably damaging	Het
Shox2	C	G	3: 66,888,796 (GRCm39)	G32R	probably damaging	Het
Sp3	T	A	2: 72,768,466 (GRCm39)	N766Y	probably damaging	Het
Spag7	T	A	11: 70,560,059 (GRCm39)	S17C	probably null	Het
Stk25	A	T	1: 93,563,031 (GRCm39)	F7I	probably benign	Het
Tbx15	G	A	3: 99,259,880 (GRCm39)	G584S	probably benign	Het
Tenm2	T	C	11: 36,755,503 (GRCm39)	D165G	probably benign	Het
Tox2	C	A	2: 163,046,649 (GRCm39)	S42*	probably null	Het
Vmn1r39	A	G	6: 66,781,754 (GRCm39)	V188A	probably damaging	Het
Zbtb5	A	T	4: 44,993,941 (GRCm39)	M481K	probably benign	Het
Zfp26	T	C	9: 20,355,615 (GRCm39)	T56A	possibly damaging	Het
Zfp459	C	A	13: 67,556,498 (GRCm39)	C195F	probably damaging	Het
Zfp703	C	T	8: 27,469,233 (GRCm39)	P299L	probably damaging	Het
Zfp764	A	G	7: 127,004,105 (GRCm39)	I342T	probably benign	Het
Zfp942	T	C	17: 22,151,985 (GRCm39)	N7D	probably null	Het

Other mutations in Kdm1a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00796:Kdm1a	APN	4	136,281,558 (GRCm39)	missense	probably damaging	1.00
IGL01106:Kdm1a	APN	4	136,299,639 (GRCm39)	splice site	probably benign
IGL01356:Kdm1a	APN	4	136,281,202 (GRCm39)	missense	probably damaging	1.00
IGL01886:Kdm1a	APN	4	136,288,327 (GRCm39)	critical splice donor site	probably null
IGL02605:Kdm1a	APN	4	136,278,348 (GRCm39)	unclassified	probably benign
IGL02885:Kdm1a	APN	4	136,279,846 (GRCm39)	missense	probably benign	0.00
Seven_falls	UTSW	4	136,295,911 (GRCm39)	nonsense	probably null
R0095:Kdm1a	UTSW	4	136,278,205 (GRCm39)	missense	probably benign	0.09
R0532:Kdm1a	UTSW	4	136,288,377 (GRCm39)	missense	probably damaging	1.00
R0553:Kdm1a	UTSW	4	136,282,609 (GRCm39)	missense	probably damaging	1.00
R3625:Kdm1a	UTSW	4	136,288,419 (GRCm39)	missense	possibly damaging	0.93
R4085:Kdm1a	UTSW	4	136,279,273 (GRCm39)	nonsense	probably null
R4285:Kdm1a	UTSW	4	136,309,347 (GRCm39)	splice site	probably null
R5118:Kdm1a	UTSW	4	136,284,669 (GRCm39)	unclassified	probably benign
R5800:Kdm1a	UTSW	4	136,300,381 (GRCm39)	splice site	probably null
R5945:Kdm1a	UTSW	4	136,296,012 (GRCm39)	splice site	probably null
R6256:Kdm1a	UTSW	4	136,295,911 (GRCm39)	nonsense	probably null
R6508:Kdm1a	UTSW	4	136,281,621 (GRCm39)	missense	probably damaging	1.00
R7243:Kdm1a	UTSW	4	136,279,265 (GRCm39)	missense	probably damaging	1.00
R7270:Kdm1a	UTSW	4	136,279,838 (GRCm39)	missense	probably damaging	0.97
R7723:Kdm1a	UTSW	4	136,285,060 (GRCm39)	missense	probably benign	0.06
R8391:Kdm1a	UTSW	4	136,281,154 (GRCm39)	missense	probably benign	0.45
R8698:Kdm1a	UTSW	4	136,286,518 (GRCm39)	missense	probably benign	0.00
R8840:Kdm1a	UTSW	4	136,287,716 (GRCm39)	missense	probably damaging	1.00
R9146:Kdm1a	UTSW	4	136,329,739 (GRCm39)	missense	unknown
R9778:Kdm1a	UTSW	4	136,279,892 (GRCm39)	missense	probably damaging	0.98
X0066:Kdm1a	UTSW	4	136,286,536 (GRCm39)	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- AGCTGAAGCAGTATCAGGCG -3'
(R):5'- TGGGATCAGGTAGGACTTCTTC -3'

Sequencing Primer
(F):5'- GGCGGAGCAATTAATTGC -3'
(R):5'- GAACATATTTGAGAACTGCGTGTG -3'

Posted On

2016-10-05