Whole-exome sequencing identifies new pathogenic germline variants in patients with colorectal polyposis

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Aug 7, 2025 (publication date) through Aug 28, 2025

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World Journal of Gastroenterology

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1007-9327

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

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World J Gastroenterol. Aug 7, 2025; 31(29): 104830
Published online Aug 7, 2025. doi: 10.3748/wjg.v31.i29.104830

Table 2 Pathogenic and likely pathogenic variants identified in the participants of study

Index case	Polyposis/tumor (age at diagnosis)	Gene	Transcript	cDNA change	Protein change	Revel	GnomAD AF	Classification¹
1165	Attenuated polyposis (53)/CRC (52)	PCSK7	NM_004716.3	c.1054+1del	-	NP	NR	P
1488	Attenuated polyposis (40)/endometrium hyperplasia (50)	DKK4	NM_014420.3	c.108del	p.(Lys37Argfs50)	NP	NR	LP
		NTHL1	NM_002528.7	c.244C>T	p.(Gln82)	NP	1.40e-03	P
		PIDD1	NM_145886.3	c.2042-2A>G	-	NP	8.41e-05	LP
1490	Attenuated polyposis (52)	ST7 L	NM_017744.5	c.540dup	p.(Tyr181Ilefs3)	NP	NR	LP
1536	Breast (58)/attenuated polyposis (63)	CD44	NM_001001392.2	c.250C>T	p.(Gln84)	NP	NR	LP
1536	Breast (58)/attenuated polyposis (63)	TG	NM_003235.5	c.4588C>T	p.(Arg1530)	0.329	8.354e-05	LP
1831	Attenuated polyposis (36)	HLTF	NM_003071.3	c.1160+2T>C	-	NP	3.98E-06	P
1831	Attenuated polyposis (36)	MUC16	NM_024690.2	c.14516del	p.(Gly4839Valfs55)	NP	8.032e-06	LP
2325	Attenuated polyposis (59)/CRC (59)	OBSCN	NM_001271223.2	c.3574C>T	p.(Gln119)	NP	NR	LP
2448	Attenuated polyposis (19)/CRC (19)	PMS2	NM_000535.7	c.1882C>T	p.(Arg628)	NP	1.59E-05	P
278	Attenuated polyposis (55)/CRC (55)	MUC16	NM_024690.2	c.14338_14341del	p.(Thr4780 Leufs4)	NP	1.21E-05	LP
278	Attenuated polyposis (55)/CRC (55)	TINF2	NM_001099274.3	c.1202dup	p.(Asn401 Lysfs19)	NP	NR	LP
454	Classic polyposis (19)	FRK	NM_002031.3	c.190C>T	p.(Arg64)	NP	1.591e-05	LP
517	Attenuated polyposis (56)	PNKP	NM_007254.4	c.1541_1548dup	p.(Gln517Cysfs)	NP	NR	P
547	Attenuated polyposis (51)/CRC (51)	A1CF	NM_014576.4	c.826C>T	p.(Arg276)	NP	7.982e-06	LP
907	Attenuated polyposis (61)	AHRR	NM_001377236.1	c.938C>A	p.(Ser313)	NP	NR	LP

¹Classification according to American College of Medical Genetics and Genomics criteria[25].

AF: Allele frequency; NP: Not predicted; NR: Not reported; P: Pathogenic; LP: Likely pathogenic.

Citation: dos Santos W, Pereira AS, Laureano T, de Andrade ES, Reis MT, Garcia FA, Campacci N, Melendez ME, Reis RM, Galvão HC, Palmero EI. Whole-exome sequencing identifies new pathogenic germline variants in patients with colorectal polyposis. World J Gastroenterol 2025; 31(29): 104830
URL: https://www.wjgnet.com/1007-9327/full/v31/i29/104830.htm
DOI: https://dx.doi.org/10.3748/wjg.v31.i29.104830