Mutagenetix > Incidental Mutation

Incidental Mutation 'R9146:Kdm1a'

694629

Institutional Source

Beutler Lab

Gene Symbol

Kdm1a

Ensembl Gene

ENSMUSG00000036940

Gene Name

lysine (K)-specific demethylase 1A

Synonyms

1810043O07Rik, Kdm1, LSD1, Aof2

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9146 (G1)

Quality Score

220.009

Status

Not validated

Chromosome

Chromosomal Location

136277851-136330034 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 136329739 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Lysine at position 53 (T53K)

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

SMART Domains

Protein: ENSMUSP00000101473
Gene: ENSMUSG00000036940
AA Change: T53K

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

unknown
Transcript: ENSMUST00000116273
AA Change: T53K

SMART Domains

Protein: ENSMUSP00000111977
Gene: ENSMUSG00000036940
AA Change: T53K

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

98% (54/55)

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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ache	G	A	5: 137,289,077 (GRCm39)	G261D	probably damaging	Het
Adgrv1	T	A	13: 81,561,291 (GRCm39)	T5408S	probably benign	Het
Aff3	T	C	1: 38,359,200 (GRCm39)	N362D	probably benign	Het
Aff4	A	G	11: 53,298,963 (GRCm39)	N956S	probably benign	Het
Alg10b	A	G	15: 90,112,401 (GRCm39)	E415G	probably damaging	Het
Ate1	T	C	7: 130,069,022 (GRCm39)	Y415C	probably damaging	Het
Cage1	T	C	13: 38,207,005 (GRCm39)	D280G	probably benign	Het
Catsperg1	G	C	7: 28,909,912 (GRCm39)	P72R	probably benign	Het
Cep290	A	G	10: 100,377,665 (GRCm39)	E1565G	probably benign	Het
Csmd1	T	A	8: 16,048,832 (GRCm39)	Y2290F	probably benign	Het
Cyp2c39	A	T	19: 39,527,344 (GRCm39)	H230L		Het
Efhb	A	G	17: 53,769,644 (GRCm39)	S222P	probably benign	Het
Emilin2	G	A	17: 71,581,331 (GRCm39)	T465M	probably damaging	Het
Ep400	A	T	5: 110,849,635 (GRCm39)	Y1431*	probably null	Het
Gm10912	T	C	2: 103,897,053 (GRCm39)	V64A	possibly damaging	Het
Gpat2	T	C	2: 127,273,206 (GRCm39)	S197P	possibly damaging	Het
Hc	T	C	2: 34,924,571 (GRCm39)	Y452C	probably damaging	Het
Hectd4	T	C	5: 121,487,097 (GRCm39)	I3364T	probably benign	Het
Hjurp	TCTGGGAGGGCTTGCTCCGGGGGCAGTGTGTCCTGTTCTTGTGCAGCCCCTGCT	TCT	1: 88,194,000 (GRCm39)		probably benign	Het
Hmcn1	G	A	1: 150,474,141 (GRCm39)	T4767M	probably benign	Het
Hspa4l	A	G	3: 40,736,101 (GRCm39)	D595G	probably benign	Het
Kirrel1	T	C	3: 87,003,015 (GRCm39)	D126G	probably damaging	Het
Kit	T	A	5: 75,810,305 (GRCm39)	D822E	probably damaging	Het
Kiz	C	T	2: 146,705,740 (GRCm39)	T100M	probably benign	Het
Kmt2a	T	A	9: 44,725,938 (GRCm39)	K3663*	probably null	Het
Krt8	T	A	15: 101,907,370 (GRCm39)	I238F	probably damaging	Het
Ky	C	T	9: 102,419,405 (GRCm39)	P471S		Het
Lca5l	T	C	16: 95,960,998 (GRCm39)	E493G	probably damaging	Het
Lrrc2	C	T	9: 110,808,582 (GRCm39)	T273I	probably damaging	Het
Mcoln2	T	C	3: 145,869,303 (GRCm39)	S31P	probably benign	Het
Mmp1a	A	G	9: 7,464,997 (GRCm39)	D77G	probably damaging	Het
Mrgprb8	T	A	7: 48,039,200 (GRCm39)	C290*	probably null	Het
Nfe2l3	G	T	6: 51,410,172 (GRCm39)	A96S	probably damaging	Het
Notch2	A	G	3: 98,011,854 (GRCm39)	D624G	probably damaging	Het
Nup98	C	A	7: 101,788,037 (GRCm39)	R1011L	probably benign	Het
Nxt2	C	T	X: 141,020,747 (GRCm39)	A118V	possibly damaging	Het
Or52n2	T	A	7: 104,542,452 (GRCm39)	I128F	probably damaging	Het
Or6c7	T	C	10: 129,323,392 (GRCm39)	V171A	possibly damaging	Het
Pcdh10	G	A	3: 45,334,351 (GRCm39)	A222T	probably benign	Het
Piezo1	G	A	8: 123,227,002 (GRCm39)	H420Y		Het
Pik3r1	C	A	13: 101,825,136 (GRCm39)		probably benign	Het
Plcb1	T	A	2: 135,182,615 (GRCm39)	Y642N	probably damaging	Het
Ralgapa2	T	A	2: 146,184,252 (GRCm39)	H1538L	probably benign	Het
Raph1	A	G	1: 60,558,137 (GRCm39)		probably null	Het
Rnf213	T	C	11: 119,334,499 (GRCm39)	F3237S		Het
Sctr	A	G	1: 119,982,010 (GRCm39)	D286G	probably damaging	Het
Smyd3	A	G	1: 178,920,529 (GRCm39)	S202P	probably damaging	Het
Ssh2	G	A	11: 77,328,502 (GRCm39)	G356E	probably damaging	Het
Stat3	A	T	11: 100,784,492 (GRCm39)	S629R	probably benign	Het
Stc2	A	G	11: 31,317,847 (GRCm39)	V58A	probably damaging	Het
Tcerg1l	T	A	7: 137,831,588 (GRCm39)	D463V	probably damaging	Het
Tctn1	A	G	5: 122,389,745 (GRCm39)	V259A	possibly damaging	Het
Tmem248	A	G	5: 130,260,851 (GRCm39)	T139A	probably benign	Het
Trip12	G	T	1: 84,771,881 (GRCm39)	A89E	possibly damaging	Het
Vmn2r54	C	T	7: 12,366,647 (GRCm39)	V96I	probably benign	Het
Vmn2r79	C	T	7: 86,650,681 (GRCm39)	Q156*	probably null	Het
Zfp831	C	A	2: 174,487,461 (GRCm39)	T712N	possibly damaging	Het
Zfy1	A	T	Y: 726,033 (GRCm39)	H577Q	possibly damaging	Het
Zscan4-ps2	T	G	7: 11,251,679 (GRCm39)	S238R	possibly damaging	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
R5493:Kdm1a	UTSW	4	136,284,732 (GRCm39)	frame shift	probably null
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
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'- TTTCCCAGTCAGACCATCAGGG -3'
(R):5'- AAGTCAGGCGGATATGCTGG -3'

Sequencing Primer
(F):5'- ACCAGCGGTTCGATCACG -3'
(R):5'- ATATGCTGGGTCGCACTCC -3'

Posted On

2022-01-20