Table 3 Rare variants identified in EC and LTNP individuals.

From: Whole Exome Sequencing of HIV-1 long-term non-progressors identifies rare variants in genes encoding innate immune sensors and signaling molecules

Patient number

Gene symbol

Gene function

Gene region

Protein variant

Transcript variant

GnomAD Freq.

CADD

MSC

PP2

EC 001

         

EC 002 A*24, B*57, ∆32

         

EC 003 B*57, ∆32

         

EC 004

DDOST

Glycosylation of ENV on HIV, infectivity

Exonic

p.T400I

c.1199 C > T

0.114

32.0

3.3

Pr.D

 

TAB2

Bacterial sensing

Exonic

p.R576H

c.1727G > A

0.000

33.0

<1

Pr.D

 

MMP9

Endocytosis of HIV-1

Exonic

p.R652W

c.1954C > T

0.001

24.1

3.3

B

LTNP 005

PIK3C2B

HIV nuclear import

Exonic

p.E1169K

c.3505 G > A

0.008

27.9

3.3

B

 

FRK

HIV binding and import

Exonic

p.V362A

c.1085 T > C

0.021

27.6

3.3

Pr.D

LTNP 006 B*13,

EGF

Increases activation of HIV LTR

Exonic

p.Y903C

c.2708 A > G

0.001

26.2

3.3

Pr.D

B*27, ∆32

MAP1A

HIV nuclear import

Exonic

p.P2690S

c.8068 C > T

0.145

25.6

3.3

Pr.D

 

PIK3R5

HIV nuclear import

Exonic

p.L90V

c.268 C > G

 

26.9

3.3

Pr.D

LTNP 007

FGD6

HIV inward trafficking

Exonic

p.K46Q

c.136 A > C

0.078

22.2

3.3

Po.D

 

CMA1

Chymotryptic serine proteinase

Exonic

p.R33C

c.97 C > T

0.025

24.6

3.3

B

LTNP 008

FN1

CD4-dependent infectivity

Exonic

p.R592H

c.1775G > A

0.292

29.5

28.4

Po.D

 

LRRFIP1

Innate sensor

Exonic

p.M151V

c.451 A > G

0.002

26.3

3.3

Pr.D

 

IRAK2

Bacterial sensing

Exonic

p.P421L

c.1262 C > T

0.004

31.0

3.3

Pr.D

 

PRKDC

Interacts with Tat

Exonic

p.L1707Q

c.5120 T > A

0.217

25.4

3.3

Pr.D

 

MED6

Interacts with Tat

Exonic

p.R183G

c.547 C > G

0.000

25.4

15.8

Po.D

 

NOD2

Bacterial sensing

Exonic

p.T189M

c.566 C > T

0.230

26.0

<1

Pr.D

LTNP 009 ∆32

FN1

CD4-dependent infectivity

Exonic

p.R2425H

c.7274 G > A

0.036

34.0

28.4

B

 

FN1

CD4-dependent infectivity

Exonic

p.P2016L

c.6047 C > T

0.032

34.0

28.4

B

 

PIK3R6

HIV nuclear import

SSL

c.2109-1 G > A

0.096

25,5

3.3

  

LTNP 010 B*57

DDOST

Glycosylation of ENV on HIV, infectivity

Exonic

p.V255I

c.763 G > A

0.017

23.8

3.3

B

 

SLX4

Vpr-mediated G2/M arrest and chronic IFN production

Exonic

p.R1479*

c.4435 C > T

0.002

37.0

<1

 
 

PRKDC

Interacts with Tat

Exonic

p.L3073F

c.9217 C > T

0.095

21.2

3.3

Po.D

LTNP 011

CCNT1

Interacts with Tat

Exonic

p.R572H

c.1715G > A

0.060

27.1

3.3

Pr.D

B*13, B*13, ∆32

PRKCA

HIV nuclear import

Exonic

p.V344L

c.1030 G > T

0.005

24.9

3.3

B

  1. Variants are shown according to individual patients. No variants were identified in EC 001, EC 002, and EC 003. Full gene names and further information can be found in Supplementary Table 4. In variant annotations, stop codons are marked with*. Mutation Significance Cutoff (MSC); Combined Annotation Dependent Depletion (CADD) score; splice cite loss (SSL); frequency (Freq.); PolyPhen-2 score (PP2); Probably damaging (Pr.D); Possibly damaging (Po.D); Benign (B).
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