Mutagenetix > Incidental Mutation

Incidental Mutation 'R9778:Kdm1a'

733828

Institutional Source

Beutler Lab

Gene Symbol

Kdm1a

Ensembl Gene

ENSMUSG00000036940

Gene Name

lysine (K)-specific demethylase 1A

Synonyms

Aof2, 1810043O07Rik, Kdm1, LSD1

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9778 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

136550540-136602723 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 136552581 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Methionine at position 703 (I703M)

Ref Sequence

ENSEMBL: ENSMUSP00000111977 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001116] [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

SMART Domains

Protein: ENSMUSP00000035457
Gene: ENSMUSG00000036940
AA Change: I532M

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: I723M

PolyPhen 2 Score 0.874 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000101473
Gene: ENSMUSG00000036940
AA Change: I723M

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 damaging
Transcript: ENSMUST00000116273
AA Change: I703M

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000111977
Gene: ENSMUSG00000036940
AA Change: I703M

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 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

Coding Region Coverage

1x: 99.9%
3x: 99.8%
10x: 99.4%
20x: 98.5%

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: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310022B05Rik	A	T	8: 124,639,359	I215N	probably damaging	Het
Aig1	T	C	10: 13,653,013		probably null	Het
Atp8b2	T	A	3: 89,954,558	K82N	possibly damaging	Het
Cacnb4	T	G	2: 52,469,603	Y131S	probably damaging	Het
Cep170b	G	A	12: 112,731,430	S62N	possibly damaging	Het
Crmp1	A	G	5: 37,265,275	D142G	probably benign	Het
Csf1r	A	G	18: 61,127,885	Q716R	possibly damaging	Het
Cyp2u1	T	C	3: 131,293,484	T483A	possibly damaging	Het
D930020B18Rik	T	C	10: 121,667,660	F247L	probably benign	Het
Dcaf13	T	C	15: 39,145,191	L396P	probably damaging	Het
Dnhd1	A	G	7: 105,704,033	M2798V	probably benign	Het
E030018B13Rik	A	T	7: 63,919,377	T58S	unknown	Het
Eipr1	T	C	12: 28,847,658		probably null	Het
Elf1	C	T	14: 79,580,508	T526M	possibly damaging	Het
Gm30302	C	T	13: 49,786,066	V723M	possibly damaging	Het
Gm35339	T	A	15: 76,356,925	F574I		Het
Gm8369	GTGTGTGTGTGTGTGTGTGTG	GTGTGTGTGTGTGTGTGTGTGTG	19: 11,511,764		probably null	Het
Got1	A	G	19: 43,515,845	S46P	probably benign	Het
Inpp4b	T	C	8: 82,048,531	I786T	probably benign	Het
Krt222	A	T	11: 99,235,012	S264R	probably benign	Het
Lrrd1	A	C	5: 3,849,982	S96R	possibly damaging	Het
Ltb	C	A	17: 35,195,930	Y235*	probably null	Het
Mbd2	T	A	18: 70,617,979	C362S	probably damaging	Het
Mlycd	T	A	8: 119,402,586	I264N	probably damaging	Het
Mri1	C	T	8: 84,254,304	C199Y	possibly damaging	Het
Muc5ac	A	T	7: 141,795,284	K487*	probably null	Het
Myh13	T	C	11: 67,358,190	I1274T	probably damaging	Het
Ncdn	G	A	4: 126,748,674	R397W	probably damaging	Het
Ncf1	T	A	5: 134,229,590		probably benign	Het
Nipbl	C	A	15: 8,291,548	A2692S	probably benign	Het
Odf2l	C	T	3: 145,149,028	T542I	possibly damaging	Het
Olfr118	T	A	17: 37,672,254	I77N	probably damaging	Het
Olfr517	A	G	7: 108,868,491	I221T	probably damaging	Het
Oxsm	T	C	14: 16,242,629	T47A	possibly damaging	Het
Pcdhga3	A	T	18: 37,674,733	S80C	probably benign	Het
Pcnx2	T	C	8: 125,785,437	T1377A	probably benign	Het
Phactr3	C	A	2: 178,283,012	Q252K	possibly damaging	Het
Phf2	T	C	13: 48,819,625	H385R	unknown	Het
Pkd1l3	A	T	8: 109,631,305	T820S	probably benign	Het
Plekhg1	T	A	10: 3,937,966	H353Q		Het
Prss37	T	A	6: 40,517,779	E24V	probably damaging	Het
Reln	A	G	5: 21,950,945	F2183S	probably damaging	Het
Slc20a2	A	G	8: 22,561,391	D480G	probably damaging	Het
Slc8a2	C	T	7: 16,153,199	T672M	probably damaging	Het
Slf2	A	G	19: 44,973,227	T1062A	probably benign	Het
Snx29	A	G	16: 11,405,745	E18G	possibly damaging	Het
Srf	C	A	17: 46,549,153	G482V	possibly damaging	Het
Styk1	G	A	6: 131,311,029	Q124*	probably null	Het
Tcf7l1	G	T	6: 72,631,243	A385E	probably damaging	Het
Thbs4	A	G	13: 92,776,987	S142P	probably benign	Het
Tlr1	G	A	5: 64,926,028	S402F	probably damaging	Het
Tnrc6a	A	G	7: 123,170,412	H475R	probably benign	Het
Trmt10b	A	T	4: 45,314,374	N272I	probably damaging	Het
Ubxn7	A	T	16: 32,381,653	N409I	probably benign	Het
Vcan	T	C	13: 89,689,811	E2538G	probably damaging	Het
Vmn1r65	C	T	7: 6,008,388	W282*	probably null	Het
Vmn2r4	A	G	3: 64,415,076	I74T	probably benign	Het
Zfp949	T	C	9: 88,567,287		probably null	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
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
X0066:Kdm1a	UTSW	4	136559225	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- TCCTGGTCAAGAACTTAAGCTGC -3'
(R):5'- TATTGCTTGCCATTGCCATG -3'

Sequencing Primer
(F):5'- GCCAAAACCCTAGTTCGGTTG -3'
(R):5'- CCATGGAGCCCTTTAAGTGATCAG -3'

Posted On

2022-11-14