Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02103:Kdm5c'

279836

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Kdm5c

Ensembl Gene

ENSMUSG00000025332

Gene Name

lysine demethylase 5C

Synonyms

D930009K15Rik, Jarid1c, Smcx

Accession Numbers

Essential gene?

Not available question?

Stock #

IGL02103

Quality Score

Status

Chromosome

Chromosomal Location

151016016-151057531 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 151031762 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 408 (F408L)

Ref Sequence

ENSEMBL: ENSMUSP00000080814 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000082177] [ENSMUST00000112584] [ENSMUST00000112588]

AlphaFold

P41230

Predicted Effect

probably damaging
Transcript: ENSMUST00000082177
AA Change: F408L

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000080814
Gene: ENSMUSG00000025332
AA Change: F408L

Domain	Start	End	E-Value	Type
JmjN	13	54	3.45e-23	SMART
ARID	21	124	1.6e-9	SMART
PHD	285	331	4.28e-13	SMART
JmjC	427	593	6.31e-64	SMART
Pfam:zf-C5HC2	666	719	2.8e-19	PFAM
Pfam:PLU-1	730	1059	6.6e-102	PFAM
low complexity region	1134	1145	N/A	INTRINSIC
PHD	1146	1207	6.01e-8	SMART
low complexity region	1349	1360	N/A	INTRINSIC
low complexity region	1397	1417	N/A	INTRINSIC
low complexity region	1436	1462	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000112584
AA Change: F449L

PolyPhen 2 Score 0.898 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000108203
Gene: ENSMUSG00000025332
AA Change: F449L

Domain	Start	End	E-Value	Type
JmjN	13	54	3.45e-23	SMART
ARID	76	165	1.09e-34	SMART
BRIGHT	80	170	1.3e-34	SMART
PHD	326	372	4.28e-13	SMART
JmjC	468	634	6.31e-64	SMART
Pfam:zf-C5HC2	707	759	2.4e-18	PFAM
Pfam:PLU-1	772	1100	9.3e-91	PFAM
low complexity region	1175	1186	N/A	INTRINSIC
PHD	1187	1248	6.01e-8	SMART
low complexity region	1393	1404	N/A	INTRINSIC
low complexity region	1441	1461	N/A	INTRINSIC
low complexity region	1480	1506	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000112588
AA Change: F449L

PolyPhen 2 Score 0.898 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000108207
Gene: ENSMUSG00000025332
AA Change: F449L

Domain	Start	End	E-Value	Type
JmjN	13	54	3.45e-23	SMART
ARID	76	165	1.09e-34	SMART
BRIGHT	80	170	1.3e-34	SMART
PHD	326	372	4.28e-13	SMART
JmjC	468	634	6.31e-64	SMART
Pfam:zf-C5HC2	707	760	2.9e-19	PFAM
Pfam:PLU-1	771	1100	6.9e-102	PFAM
low complexity region	1175	1186	N/A	INTRINSIC
PHD	1187	1248	6.01e-8	SMART
low complexity region	1390	1401	N/A	INTRINSIC
low complexity region	1438	1458	N/A	INTRINSIC
low complexity region	1477	1503	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154938

Coding Region Coverage

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the regulation of transcription and chromatin remodeling. Mutations in this gene have been associated with X-linked mental retardation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
PHENOTYPE: Male chimeras hemizygous for a gene trapped allele exhibit posterior patterning defects and abnormal heart morphology at E9.5. Chimeras hemizygous for a different gene trapped allele appear normal at E10.5. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcd4	G	A	12: 84,659,138 (GRCm39)	T206M	probably benign	Het
Adcy3	T	A	12: 4,184,390 (GRCm39)	V22D	possibly damaging	Het
Alb	G	A	5: 90,611,990 (GRCm39)	E140K	probably benign	Het
Aph1a	G	A	3: 95,803,125 (GRCm39)	V193I	probably damaging	Het
Asb2	G	A	12: 103,299,755 (GRCm39)	R178*	probably null	Het
Celf3	A	T	3: 94,394,108 (GRCm39)	Q137L	probably damaging	Het
Cmya5	T	C	13: 93,228,635 (GRCm39)	D2151G	probably benign	Het
Cuedc1	T	A	11: 88,079,625 (GRCm39)	S353T	probably damaging	Het
Dlg5	A	C	14: 24,194,414 (GRCm39)	L1709R	probably damaging	Het
Dst	T	C	1: 34,229,199 (GRCm39)	I1939T	possibly damaging	Het
Emx2	A	T	19: 59,450,130 (GRCm39)	N149I	probably benign	Het
Fancm	A	G	12: 65,142,558 (GRCm39)	D472G	probably benign	Het
Fasn	T	C	11: 120,702,762 (GRCm39)	Y1700C	probably damaging	Het
Fat2	T	A	11: 55,180,122 (GRCm39)	R1406S	probably damaging	Het
Fat4	C	A	3: 38,943,348 (GRCm39)	T747K	probably damaging	Het
Fer	A	G	17: 64,445,923 (GRCm39)	M795V	probably benign	Het
Gm5916	A	G	9: 36,039,970 (GRCm39)	L6P	probably damaging	Het
Gpr139	A	G	7: 118,744,355 (GRCm39)	F77L	possibly damaging	Het
Kcnu1	T	C	8: 26,395,976 (GRCm39)	S654P	possibly damaging	Het
Kel	A	G	6: 41,679,323 (GRCm39)	S147P	probably benign	Het
Klra5	A	T	6: 129,888,307 (GRCm39)		probably null	Het
Mastl	A	G	2: 23,030,010 (GRCm39)	S239P	probably benign	Het
Med18	A	T	4: 132,186,977 (GRCm39)	V174D	probably damaging	Het
Mgat4a	A	T	1: 37,502,007 (GRCm39)	M247K	possibly damaging	Het
Mx2	A	C	16: 97,345,795 (GRCm39)	D71A	probably damaging	Het
Nxt1	G	T	2: 148,517,564 (GRCm39)	E102*	probably null	Het
Or14j1	A	G	17: 38,146,169 (GRCm39)	Q93R	possibly damaging	Het
Or3a1	A	G	11: 74,225,862 (GRCm39)	F65S	probably damaging	Het
Or7g16	T	C	9: 18,727,005 (GRCm39)	N195S	probably damaging	Het
Pcdhb16	T	A	18: 37,613,161 (GRCm39)	V707E	probably benign	Het
Pdzrn4	T	A	15: 92,667,768 (GRCm39)	V640E	probably damaging	Het
Piwil4	T	C	9: 14,637,282 (GRCm39)		probably null	Het
Pla2g4a	A	T	1: 149,776,950 (GRCm39)	D55E	probably damaging	Het
Plekhg2	C	A	7: 28,059,501 (GRCm39)	R1276L	probably damaging	Het
Psd4	G	A	2: 24,290,540 (GRCm39)	W539*	probably null	Het
Rae1	G	A	2: 172,845,306 (GRCm39)	E33K	probably damaging	Het
Rbm12b1	T	A	4: 12,145,563 (GRCm39)	F512I	probably damaging	Het
Rfx6	A	G	10: 51,602,952 (GRCm39)	D823G	possibly damaging	Het
Samt3	A	T	X: 85,090,759 (GRCm39)	Q217L	probably damaging	Het
Selenbp2	A	G	3: 94,605,438 (GRCm39)	N134S	probably null	Het
Selenoo	T	C	15: 88,984,173 (GRCm39)	V663A	probably damaging	Het
Sp4	G	T	12: 118,263,284 (GRCm39)	T254N	probably damaging	Het
Spdya	A	G	17: 71,885,242 (GRCm39)	K232R	probably benign	Het
Stom	A	T	2: 35,210,401 (GRCm39)	V201E	probably benign	Het
Sycp3	A	G	10: 88,302,334 (GRCm39)	K108R	possibly damaging	Het
Usp2	A	G	9: 44,000,425 (GRCm39)		probably benign	Het
Vmn1r226	T	C	17: 20,907,926 (GRCm39)	S53P	probably damaging	Het
Vmn2r14	C	T	5: 109,372,349 (GRCm39)	G47D	probably damaging	Het
Vwf	T	G	6: 125,623,318 (GRCm39)	L1805W	probably damaging	Het
Washc3	A	T	10: 88,037,687 (GRCm39)	Q22L	probably damaging	Het
Wdr81	T	A	11: 75,335,546 (GRCm39)	D1761V	probably damaging	Het

Other mutations in Kdm5c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02434:Kdm5c	APN	X	151,016,558 (GRCm39)	start codon destroyed	probably null	0.87
IGL02456:Kdm5c	APN	X	151,029,314 (GRCm39)	missense	probably damaging	1.00

Posted On

2015-04-16