DUSP5 and PHLDA1 mutations in mature cystic teratomas of the ovary identified on whole-exome sequencing may explain teratoma characteristics

Wang, Wen-Chung; Lai, Yen-Chein

doi:10.1186/s40246-022-00424-w

Human Genomics

Table 2 Common genetic variants detected in all 9 paraffin-embedded tumor specimens on whole-exome sequencing

From: DUSP5 and PHLDA1 mutations in mature cystic teratomas of the ovary identified on whole-exome sequencing may explain teratoma characteristics

#chr	Position	Variation	REF	ALT	Depth	SA_AF	Impact	Symbol	E/I	Class	Consequence	HGVS nomenclature	HGVSp nomenclature
Exon
chr1	117487710	rs71483896	AT	GA	631	None	Moderate	PTGFRN	3/9	Substitution	Missense variant	c.828_829delinsGA	p.Ser277Thr
chr2	133074851	rs7355688	A	T	224	None	Modifier	ZNF806	3/3	SNV	Non-coding transcript exon variant	n.316A>T
chr2	240981375	rs6732185	T	A	1044	0.08	Moderate	PRR21	1/1	SNV	Missense variant	c.1025A>T	p.Lys342Met
chr10	112266822	rs35834951	GC	AT	760	None	Moderate	DUSP5	3/4	Substitution	Missense variant	c.658_659delinsAT	p.Ala220Met
chr12	76424937	rs71716769	TTGC	T	615	None	Moderate	PHLDA1	1/2	Deletion	Inframe deletion	c.582_584del	p.Gln204del
chr15	23686673	rs59122400	G	A	745	0.67	Moderate	GOLGA6L2	8/8	SNV	Missense variant	c.949C>T	p.Arg317Trp
chr16	12021332	rs256390	G	A	1122	0.68	Low	RP11-166B2.1	8/8	SNV	Synonymous variant	c.1092C>T	p.Pro364Pro
chr17	39334133	rs389784	T	C	985	None	Moderate	KRTAP4-2	1/1	SNV	Missense variant	c.284A>G	p.Tyr95Cys
chr17	41960633	rs70964679	CG	GC	727	None	Moderate	MPP2	4/13	Substitution	Missense variant	c.240_241delinsGC	p.His80_Val81delinsGlnLeu
chr17	46973139	rs35074390	TG	T	586	1.0	Modifier	ATP5G1	5/5	Deletion	3′ UTR variant	c.*15delG
chr19	13319693	rs16051	A	G	209	0.21	Low	CACNA1A	46/47	SNV	Synonymous variant	c.6657 T>C	p.His2219His
chr22	29885861	rs165923	T	C	1076	0.00	Low	NEFH	4/4	SNV	Synonymous variant	c.2232 T>C	p.Ala744Ala
Intron
chr2	209049840	rs10804167	C	T	173	0.68	Modifier	C2orf80	2/8	SNV	Intron variant	c.42-84G>A
chr3	194991220	rs370476236	AA	GC	131	None	Modifier	XXYLT1	1/3	Substitution	Intron variant	c.504+63_504+64delinsGC
chr5	176895817	rs386695380	GC	AA	502	None	Modifier	DBN1	3/14	Substitution	Intron variant	c.148+27_148+28delinsTT-
chr7	75614863	rs71526806	TG	CT	394	None	Modifier	POR	12/15	Substitution	Intron variant	c.1399-34_1399-33delinsCT
chr12	51034721	rs2731436	C	T	186	None	Modifier	DIP2B	3/37	SNV	Intron variant	c.301+86C>T
chr12	132323294	rs4964884	T	C	211	0.80	Low	MMP17	3/9	SNV	Splice region variant Intron variant	c.422+8T>C
chr17	79477898	rs59886367	GC	G	1076	0.03	Modifier	ACTG1	4/4	Deletion	Intron variant	c.985-40del
chr20	2633404	rs6115307	C	G	181	0.00	Modifier	NOP56	1/11	SNV	Intron variant	c.4-84C>G
chr20	3657803	rs71212741	AT	GA	611	None	Modifier	ADAM33	2/21	Substitution	Intron variant	c.178-14_178-13delinsTC
chr22	30681797	rs6147585	T	TCTGCCCCAGCCCTTGGTGCTCCCC	609	None	Modifier	GATSL3	8/8	Insertion	Intron variant	c.921+23_921+24insGGGGAGCACCAAGGGCTGGGGCAG

chr chromosome, REF reference, ALT alteration, SA_AF South Asian allele frequency, E/I Exon/Intron
Impacts: High, the variant is assumed to have great (disruptive) impact on the protein, possibly causing protein truncation or loss of function or triggering of nonsense mediated decay; moderate, a non-disruptive variant that might change protein effectiveness; modifier, non-coding variant or variant affecting non-coding genes, with predictions difficult or no evidence of impact (https://asia.ensembl.org/Help/Glossary?id=535, accessed September 2022)
Underline: variants in exons with changes in protein coding

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ISSN: 1479-7364

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