Mutagenetix > Incidental Mutation

Incidental Mutation 'R6256:Kdm1a'

506102

Institutional Source

Beutler Lab

Gene Symbol

Kdm1a

Ensembl Gene

ENSMUSG00000036940

Gene Name

lysine (K)-specific demethylase 1A

Synonyms

Aof2, 1810043O07Rik, Kdm1, LSD1

MMRRC Submission

044373-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R6256 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

136550540-136602723 bp(-) (GRCm38)

Type of Mutation

nonsense

DNA Base Change (assembly)

G to T at 136568600 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Stop codon at position 172 (C172*)

Gene Model

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

AlphaFold

Q6ZQ88

Predicted Effect

probably null
Transcript: ENSMUST00000046846
AA Change: C268*

SMART Domains

Protein: ENSMUSP00000035457
Gene: ENSMUSG00000036940
AA Change: C268*

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 null
Transcript: ENSMUST00000105847
AA Change: C381*

SMART Domains

Protein: ENSMUSP00000101473
Gene: ENSMUSG00000036940
AA Change: C381*

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 null
Transcript: ENSMUST00000116273
AA Change: C361*

SMART Domains

Protein: ENSMUSP00000111977
Gene: ENSMUSG00000036940
AA Change: C361*

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

probably null
Transcript: ENSMUST00000155354
AA Change: C2*

SMART Domains

Protein: ENSMUSP00000114268
Gene: ENSMUSG00000036940
AA Change: C2*

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

Predicted Effect

probably null
Transcript: ENSMUST00000170979
AA Change: C172*

SMART Domains

Protein: ENSMUSP00000131385
Gene: ENSMUSG00000036940
AA Change: C172*

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: 99.9%
3x: 99.6%
10x: 97.9%
20x: 93.5%

Validation Efficiency

99% (74/75)

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: 46 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700030K09Rik	A	T	8: 72,451,428	Q361L	probably damaging	Het
Abca7	A	G	10: 80,002,622	T577A	probably damaging	Het
Acad12	A	T	5: 121,614,086	V54E	probably benign	Het
Ago4	A	G	4: 126,520,226	Y91H	probably damaging	Het
Akr1b10	T	C	6: 34,387,688	V28A	probably damaging	Het
Ccdc33	T	A	9: 58,101,918		probably null	Het
Ccdc7a	T	C	8: 128,935,593		probably null	Het
Ces1f	A	T	8: 93,265,794	V343E	probably damaging	Het
Cftr	T	C	6: 18,274,661	L896P	probably damaging	Het
Csmd3	G	A	15: 47,669,729	P2375S	probably damaging	Het
Dnajb14	G	C	3: 137,908,362	A345P	probably damaging	Het
Dnajb14	C	T	3: 137,908,363	A345V	probably damaging	Het
Dnase1	G	A	16: 4,037,621	R24K	probably benign	Het
Dnmbp	C	T	19: 43,852,281	V560M	probably damaging	Het
Dopey2	T	A	16: 93,807,214	I1981N	possibly damaging	Het
Eif3a	A	C	19: 60,771,026	S770A	possibly damaging	Het
Fbxl7	A	T	15: 26,553,002	C60S	probably benign	Het
Fras1	A	T	5: 96,733,843	D2478V	possibly damaging	Het
Hrnr	A	G	3: 93,322,611	D52G	probably damaging	Het
Jmjd1c	T	A	10: 67,220,408	L823M	probably damaging	Het
Kdm6b	C	T	11: 69,406,729	E295K	probably damaging	Het
Mepe	A	T	5: 104,337,074	M27L	probably benign	Het
Mogat2	A	T	7: 99,219,895	H305Q	probably damaging	Het
Mst1r	T	A	9: 107,917,266	Y1215N	probably damaging	Het
Muc5ac	A	T	7: 141,789,795	H48L	possibly damaging	Het
Myo7b	T	C	18: 31,983,695	D953G	probably damaging	Het
Ocel1	T	C	8: 71,371,828		probably benign	Het
Pcdhb6	A	G	18: 37,335,925	D633G	probably damaging	Het
Ppm1l	A	G	3: 69,497,897	I176V	probably benign	Het
Sall3	C	T	18: 80,969,861	R1120H	possibly damaging	Het
Sbf1	G	A	15: 89,300,867	P1018S	probably benign	Het
Setbp1	T	C	18: 78,857,257	Y1065C	probably damaging	Het
Slc25a2	T	C	18: 37,637,723		probably null	Het
Slc4a2	C	A	5: 24,435,890	T729K	probably damaging	Het
Sptlc2	T	C	12: 87,355,531	E207G	probably damaging	Het
Sult6b1	A	T	17: 78,906,914	F27I	probably benign	Het
Syf2	A	T	4: 134,934,578	K84N	probably damaging	Het
Tmem209	A	T	6: 30,497,167	N183K	probably benign	Het
Tmem232	G	T	17: 65,478,402	Q188K	possibly damaging	Het
Tomm70a	A	T	16: 57,152,692	T598S	probably benign	Het
Ttll13	A	G	7: 80,258,304	T556A	probably benign	Het
Vmn2r120	A	T	17: 57,524,700	L363*	probably null	Het
Xpo6	G	T	7: 126,108,619	Q872K	probably damaging	Het
Xrra1	A	C	7: 99,914,464	S553R	probably damaging	Het
Zfy1	A	T	Y: 738,765	V147E	unknown	Homo
Zfy2	T	C	Y: 2,116,267	I258V	probably benign	Homo

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
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
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'- GCCTAGGCAGACATGTAAATTTG -3'
(R):5'- CACCAAGGCTGAATTTAGCAAG -3'

Sequencing Primer
(F):5'- GCAGACATGTAAATTTGCACATATAC -3'
(R):5'- CCAAGGCTGAATTTAGCAAGTTTTTG -3'

Posted On

2018-02-28