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Table 3 Preliminary genetics findings for the suspected MSMD patients

From: Phenotypic and immune functional profiling of patients with suspected Mendelian Susceptibility to Mycobacterial Disease in South Africa

Patient

WES performed?

WES Result- Gene(s) & Variant(s)

rsID

Transcript ID

Zygosity

Global minor allele frequency

Clinical significance (ClinVar)

PID01

N/A

IFNGR1 (c.818del4)

rs587776856

NM_000416.3

Heterozygous

Unknown

Pathogenic

PID02

Yes

IFNGR1 (c.864C > G p.Ile288Met)

rs121913184

NM_000416.3

Heterozygous

0.00003594

Not provided

NOD2 (c.374C > T p.Pro125Leu)

rs149390911

NM_001370466.1

Heterozygous

0.0002979

Likely benign

PID03

Yes

IKZF1 (c.1009G > A p.Gly337Ser)

rs148169768

NM_006060.6

Homozygous

0.000717

Not reported in ClinVar

IFNGR1 (c.698A > C p.Gly233Ala)

rs767099047

NM_000416.3

Heterozygous

0.000003978

Not reported in ClinVar

PID04

Yes

No result

N/A

N/A

N/A

N/A

N/A

PID05

Yes

No result

N/A

N/A

N/A

N/A

N/A

PID06

Yes

IL12B (c.320A > G p.Lys107Arg)

None

NM_002187.3

Heterozygous

Unknown

Not reported in ClinVar

NFKB2 (c.2042C > T p.Pro681Leu)

rs534798782

NM_001322934.2

Heterozygous

0.00003211

Not reported in ClinVar

PID07

Yes

IL12B (c.863G > C p.Arg288Thr)

None

NM_002187.3

Homozygous

0.00111

Not reported in ClinVar

PID08

Yes

IFNGR2 (c.708A > T p.Glu236Asp)

rs121913212

NM_005534.4

Homozygous

0.0007108

Variant of unknown significance

PID09

Yes

IKBKB (c.2257G > A p.Ala753Thr)

rs200977622

NM_001556.3

Homozygous

0.00001193

Variant of unknown significance

NFKB2 (c.2042C > T p.Pro681Leu)

rs534798782

NM_001322934.2

Heterozygous

0.00003211

Not reported in ClinVar

PID10

Yes

IRAK1 (c.1939C > T p.Leu647Pro)

rs113047476

NM_001569.4

Hemizygous

0.00001974

Not reported in ClinVar

PID11

Yes

IL12RB2 (c.2071A > G p. Arg691TGly & c. 1259G > A p.Gly420Glu)

rs748575002 & rs765425600

NM_001374259.2

Both Heterozygous

0.000043282 & 0.000003979

Neither reported in ClinVar

PID12

Yes

No result

N/A

N/A

N/A

N/A

N/A

PID13

Yes

No result

N/A

N/A

N/A

N/A

N/A

PID14

No

No result

N/A

N/A

N/A

N/A

N/A

PID15

No

N/A

N/A

N/A

N/A

N/A

N/A

PID16

No

N/A

N/A

N/A

N/A

N/A

N/A