Mutagenetix > Incidental Mutation

Incidental Mutation 'R7243:Kdm1a'

563343

Institutional Source

Beutler Lab

Gene Symbol

Kdm1a

Ensembl Gene

ENSMUSG00000036940

Gene Name

lysine (K)-specific demethylase 1A

Synonyms

1810043O07Rik, Kdm1, LSD1, Aof2

MMRRC Submission

045307-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7243 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

136277851-136330034 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 136279265 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 765 (V765A)

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: V594A

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 damaging
Transcript: ENSMUST00000105847
AA Change: V785A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000101473
Gene: ENSMUSG00000036940
AA Change: V785A

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: V765A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000111977
Gene: ENSMUSG00000036940
AA Change: V765A

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

Meta Mutation Damage Score

0.7240

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

99% (73/74)

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acap1	G	A	11: 69,781,297 (GRCm39)	H103Y	probably benign	Het
Adamdec1	A	G	14: 68,809,203 (GRCm39)	M253T	probably benign	Het
Alox15	C	A	11: 70,241,540 (GRCm39)	G114C	probably null	Het
Aox3	G	T	1: 58,177,466 (GRCm39)	G227V	unknown	Het
Atp8a2	A	T	14: 59,885,291 (GRCm39)	N1144K	probably benign	Het
Cacna1c	C	T	6: 118,614,690 (GRCm39)		probably null	Het
Cog6	A	T	3: 52,909,736 (GRCm39)	W314R	probably damaging	Het
Col5a2	A	G	1: 45,415,320 (GRCm39)	I1473T	probably benign	Het
Csmd1	T	A	8: 15,965,357 (GRCm39)	D3218V	probably damaging	Het
Cyp3a11	A	G	5: 145,795,613 (GRCm39)	M446T	probably damaging	Het
Dhps	A	G	8: 85,801,567 (GRCm39)	Y340C	probably benign	Het
Dnah7b	A	G	1: 46,122,914 (GRCm39)	N108S	probably benign	Het
Dnajb1	C	T	8: 84,337,393 (GRCm39)	P323L	probably damaging	Het
Dspp	TGACAGCAGTGACAGCAGCGACAGCAGCGACAGCAGTGACAGCAGCGACAGCAGCGACAGCAGTGACAGCAGCGACAGCAGCAACAGCAGTGACAGCAG	TGACAGCAGTGACAGCAGCGACAGCAGCGACAGCAGTGACAGCAGCGACAGCAGCAACAGCAGTGACAGCAG	5: 104,326,227 (GRCm39)		probably benign	Het
Dync2h1	G	T	9: 7,102,405 (GRCm39)	T2665K	possibly damaging	Het
Etv1	C	T	12: 38,907,045 (GRCm39)	S349L	probably benign	Het
Fam171a1	A	T	2: 3,119,653 (GRCm39)	T21S	probably benign	Het
Fbh1	T	A	2: 11,756,336 (GRCm39)	T749S	probably benign	Het
Fcho2	T	C	13: 98,891,724 (GRCm39)	D346G	possibly damaging	Het
Fcrl5	A	G	3: 87,349,552 (GRCm39)	H109R	probably benign	Het
Fstl1	A	G	16: 37,647,088 (GRCm39)	S153G	probably benign	Het
Fyb1	T	C	15: 6,673,180 (GRCm39)	F605L	probably benign	Het
Gcat	T	A	15: 78,921,063 (GRCm39)	M363K	possibly damaging	Het
Gm10604	T	C	4: 11,980,113 (GRCm39)	T64A	unknown	Het
Grin2d	A	G	7: 45,515,552 (GRCm39)	L147P	probably damaging	Het
Ift88	A	T	14: 57,667,993 (GRCm39)		probably null	Het
Ighg1	A	T	12: 113,294,066 (GRCm39)	C26S		Het
Ing2	A	G	8: 48,127,574 (GRCm39)	S48P	probably damaging	Het
Kat6a	C	T	8: 23,428,791 (GRCm39)	T1382I	probably benign	Het
Klk1b26	T	C	7: 43,665,691 (GRCm39)	S168P	not run	Het
Klk1b26	A	G	7: 43,666,337 (GRCm39)	N260S	probably damaging	Het
Lama3	G	A	18: 12,552,902 (GRCm39)	G438D	probably damaging	Het
Larp6	T	A	9: 60,620,569 (GRCm39)	D27E	probably benign	Het
Lrba	T	A	3: 86,658,823 (GRCm39)		probably null	Het
Lrig2	A	T	3: 104,404,883 (GRCm39)		probably null	Het
Megf9	T	C	4: 70,353,708 (GRCm39)	E366G	probably benign	Het
Mob1b	T	A	5: 88,891,304 (GRCm39)	D52E	probably damaging	Het
Ndufb3	A	T	1: 58,630,282 (GRCm39)	H11L	unknown	Het
Odc1	T	G	12: 17,600,058 (GRCm39)	Y407*	probably null	Het
Ogfr	GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG	GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG	2: 180,237,059 (GRCm39)		probably benign	Het
Opa1	A	G	16: 29,405,814 (GRCm39)	I126M	probably benign	Het
Or2t47	T	C	11: 58,442,227 (GRCm39)	I279M	probably damaging	Het
Or3a1b	T	A	11: 74,012,559 (GRCm39)	V148E	probably damaging	Het
Or51a10	A	G	7: 103,698,962 (GRCm39)	Y200H	probably damaging	Het
Or51f5	A	T	7: 102,430,865 (GRCm39)	T61S	probably benign	Het
Pcca	A	G	14: 123,114,186 (GRCm39)	H633R	probably benign	Het
Pcdhb22	A	G	18: 37,653,685 (GRCm39)	R461G	probably benign	Het
Pcf11	A	T	7: 92,309,268 (GRCm39)	D647E	probably damaging	Het
Plscr1l1	A	G	9: 92,225,726 (GRCm39)	Y16C	probably damaging	Het
Plxnd1	T	A	6: 115,949,468 (GRCm39)	I773F	probably benign	Het
Prl8a1	A	T	13: 27,766,086 (GRCm39)	L3Q	probably damaging	Het
Psg17	C	A	7: 18,552,640 (GRCm39)	G212C	probably damaging	Het
Ptbp2	G	T	3: 119,546,761 (GRCm39)	N40K	possibly damaging	Het
Ptprj	T	C	2: 90,276,765 (GRCm39)	H1102R	probably damaging	Het
Rbfox3	T	C	11: 118,404,100 (GRCm39)	Y33C	probably damaging	Het
Ros1	T	A	10: 51,999,477 (GRCm39)	N1158Y	probably damaging	Het
Rpgrip1l	T	C	8: 91,996,751 (GRCm39)	I710V	probably benign	Het
Scn9a	A	G	2: 66,370,874 (GRCm39)	F569L	probably damaging	Het
Slc12a4	A	T	8: 106,680,552 (GRCm39)	M190K	probably damaging	Het
Slc22a20	G	A	19: 6,021,599 (GRCm39)	R468C	probably damaging	Het
Slc45a2	T	A	15: 11,023,436 (GRCm39)	Y347N	possibly damaging	Het
Slc4a10	A	G	2: 62,134,206 (GRCm39)	Y974C	probably damaging	Het
Snap47	A	G	11: 59,319,548 (GRCm39)	S197P	probably benign	Het
Snph	T	C	2: 151,436,173 (GRCm39)	S252G	probably damaging	Het
Spns2	A	T	11: 72,347,686 (GRCm39)	W335R	probably damaging	Het
Thnsl1	A	G	2: 21,217,658 (GRCm39)	I471V	probably damaging	Het
Tmprss11f	C	A	5: 86,677,975 (GRCm39)	G265C	probably damaging	Het
Tnn	C	T	1: 159,934,687 (GRCm39)	R1242H	probably benign	Het
Tsc2	T	C	17: 24,818,604 (GRCm39)	R1412G	probably benign	Het
Tsc22d2	G	T	3: 58,323,884 (GRCm39)	V259F	unknown	Het
Ttll13	A	C	7: 79,903,911 (GRCm39)	K280Q	probably damaging	Het
Wls	A	T	3: 159,615,402 (GRCm39)	I306F	possibly damaging	Het
Zfp566	A	G	7: 29,777,701 (GRCm39)	V160A	probably benign	Het
Zfyve28	T	C	5: 34,356,219 (GRCm39)	T761A	probably damaging	Het
Zswim8	G	A	14: 20,764,436 (GRCm39)	R602Q	probably 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
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'- CGGCTACATTTACAAAGCTCATGTATG -3'
(R):5'- AAGAGTAAGCAACATGGTTCTTCTC -3'

Sequencing Primer
(F):5'- CTTTCCCCAAATAGGCTC -3'
(R):5'- ACATGGTTCTTCTCACATAAATAAGG -3'

Posted On

2019-06-26