Table 2.

Variants identified by WES in combination with skeletal dysplasia-related gene-filtering in the proband.

Gene	Mutation	Mutation taster	PolyPhen-2	SIFT	1000G	gnomAD	OMIM clinical phenotype	ACMG classification
GNPTAB	c.673C>A, p.Q225K	D	B	T	—	0.00000	AR, mucolipidosis 2 alpha/beta; AR, mucolipidosis 3 alpha/beta.	BS (PM2, BS4, BP4, BP5)
TRPV4	c.2569C>A, p.Q857K	P	B	T	—	0.00002	AD, brachyolmia type 3; AD, digital arthropathy-brachydactyly, familial; AD, hereditary motor and sensory neuropathy, type 2c; AD, scapuloperoneal spinal muscular atrophy; AD, SED, Maroteaux type.	BP (BP4, BP5)
TGFB1	c.77C>T, p.P26L	D	B	T	—	—	AD, Camurati-Engelmann disease; AR, inflammatory bowel disease, immunodeficiency, and encephalopathy.	BP (PM2, BP4, BP5)
FLNB	c.2671G>A, p.D891N	P	B	T	—	0.00004	AD, atelosteogenesis, type 1/3; AD, boomerang dysplasia; AD, Larsen syndrome; AR, spondylocarpotarsal synostosis syndrome.	BP (BP4, BP5)
COL9A1	c.674A>T, p.D225V	D	B	D	0.00040	0.00025	AD, epiphyseal dysplasia, multiple, 6.	BP (BP4, BP5)
RECQL4	c.1396C>A, p.P466T	D	B	T	—	—	AR, Baller-Gerold syndrome; AR, Rothmund-Thomson syndrome, type 2.	BS (PM2, BS4, BP4, BP5)
COMP	c.1317C>G, p.D439E	D	D	D	—	—	AD, epiphyseal dysplasia, multiple, 1; AD, pseudoachondroplasia.	PS (PS1, PM1, PM2, PP1, PP3, PP4)
EVC	c.769_772delinsTTAC, p.Y258H	P	B	T	—	—	AD, Weyers acrofacial dysostosis; AR, Ellis-van Creveld syndrome.	BP (PM2, BP4, BP5)

Italicized words: mutations identified in this study; D: disease causing; B: benign; T: tolerated; P: polymorphism; AR: autosomal recessive; AD: autosomal dominant. Pathogenic: PVS1> PS1>…> PS4> PM1-6> PP1-5; benign: BA1> BS1-4> BP1-7. PVS: pathogenic very strong; PS: pathogenic strong; PM: pathogenic moderate; PP: pathogenic supporting; BA: benign stand-alone; BS, benign strong; BP, benign supporting.