Table 1. Candidate variant annotations... | Rockefeller University Press

Table 1.

Candidate variant annotations and predicted impact in patients

Patient 1 variant
Genomic position (hg38)	chr11: 119051826
Gene symbol	HYOU1
HGVSc: Nucleotide change	NM_001130991.3: c.1331C>A
HGVSp: Protein change	NP_001124463.1: p.Pro444His
gnomAD frequency	1.24.10⁻⁶ heterozygotes (no homozygotes)
PolyPhen (score)^{^a}	Probably damaging
CADD (phred score)^{^b}	16.5
GERP++_RS^{^c}	4.96
MutationTaster	Disease causing
PhastCons^{^d}	0.83
Patient 2 variant 1
Genomic position (hg38)	chr11: 119054130
Gene symbol	HYOU1
HGVSc: Nucleotide change	NM_001130991.3: c.785G>A
HGVSp: Protein change	p. Arg262Gln
gnomAD frequency	4.458.10⁻⁵
PolyPhen (score)^{^a}	Benign
CADD (phred score)^{^b}	25.3
GERP++_RS^{^c}	3.55
MutationTaster	Deleterious
PhastCons^{^d}	0.802
Patient 2 variant 2
Genomic position (hg38)	chr11: 119048352
Gene symbol	HYOU1
HGVSc: Nucleotide change	NM_001130991.3: c.2270_2272dup
HGVSp: Protein change	p. Pro757_Glu758insAla
gnomAD frequency	Absent
PolyPhen (score)^{^a}	Probably damaging
CADD (phred score)^{^b}	42
GERP++_RS^{^c}	5.54
MutationTaster	Deleterious
PhastCons^{^d}	0.869

Patient 1 variant
Genomic position (hg38)	chr11: 119051826
Gene symbol	HYOU1
HGVSc: Nucleotide change	NM_001130991.3: c.1331C>A
HGVSp: Protein change	NP_001124463.1: p.Pro444His
gnomAD frequency	1.24.10⁻⁶ heterozygotes (no homozygotes)
PolyPhen (score)^a	Probably damaging
CADD (phred score)^b	16.5
GERP++_RS^c	4.96
MutationTaster	Disease causing
PhastCons^d	0.83
Patient 2 variant 1
Genomic position (hg38)	chr11: 119054130
Gene symbol	HYOU1
HGVSc: Nucleotide change	NM_001130991.3: c.785G>A
HGVSp: Protein change	p. Arg262Gln
gnomAD frequency	4.458.10⁻⁵
PolyPhen (score)^a	Benign
CADD (phred score)^b	25.3
GERP++_RS^c	3.55
MutationTaster	Deleterious
PhastCons^d	0.802
Patient 2 variant 2
Genomic position (hg38)	chr11: 119048352
Gene symbol	HYOU1
HGVSc: Nucleotide change	NM_001130991.3: c.2270_2272dup
HGVSp: Protein change	p. Pro757_Glu758insAla
gnomAD frequency	Absent
PolyPhen (score)^a	Probably damaging
CADD (phred score)^b	42
GERP++_RS^c	5.54
MutationTaster	Deleterious
PhastCons^d	0.869

Polyphen2_HDIV_score: variants with scores between 0.85 and 1.0 are predicted to be damaging with high confidence.

CADDv1.4 scores range from 1 to 99, with a higher score indicating greater deleteriousness.

GERP++_RS score: DNA conservation score. Scores range from 1 to 6.18. The larger the score, the more conserved the site.

PhastCons score: probability of negative selection and ranges between 0 and 1.

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