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Table 4 List of all four known disease-causal variants and six probable pathogenic variants

From: An association-adjusted consensus deleterious scheme to classify homozygous Mis-sense mutations for personal genome interpretation

SNP type

Gene

Position, base change (AA change)

rsID (%MAF EA/AA/All)

Disease [prediction counts]

Grantham score

Protein stability change

Site annotations

Disease-causal

ATP6V0A4

7:138417791

rs3807153* (4.8/18.5/9.4)

Distal renal tubular acidosis (dRTA) with preserved hearing

81

Neutral

TRANSMEM

A-->G (M580T)

[Del count: 2; Con count: 3]

MTMR2

11:95569448

rs558018 (0.02/3.9/1.3)

Charcot-Marie-Tooth disease type 4B1 (CMT4B1)

46

Decrease

DOMAIN

T-->C (N545S)

[Del count: 2; Con count: 3]

APOE

19:45412079

rs7412 (5.6/8.7/6.6)

Lipoprotein glomerulopathy (LPG)

180

Decrease

REPEAT

C-->T (R176C)

[Del count: 5; Con count: 3]

BMP15

X:50658966

rs104894767 (1.4/0.3/1.0)

Premature ovarian failure type 4 (POF4)

58

Neutral

PROPEP

G-->A (A180T)

[Del count: 0; Con count: 1]

Probable pathogenic

FRZB

2:183699584

rs7775 (8.8/28.4/15.4)

Osteoarthritis type 1 (OS1)

125

Neutral

-

G-->C (R324G)

[Del count: 1; Con count: 3]

HABP2

10:115348046

rs7080536 (3.9/0.7/2.8)

[Del count: 5; Con count: 3]

98

Decrease

DOMAIN

G-->A (G534E)

HNF1A

12:121416650

rs1169288 (33.5/12.1/26.2)

Insulin-dependent diabetes mellitus type 20 (IDDM20)

5

Neutral

REGION (Dimerization)

A-->C (I27L)

[Del count: 1; Con count: 3]

XYLT1

16:17564311

rs61758388 (-/-/1.7)

[Del count: 0; Con count: 3]

99

Neutral

TOPO_DOM

C-->A (A115S)

CYP2A6

19:41354533

rs1801272 (2.5/0.5/1.8)

[Del count: 1; Con count: 3]

99

Decrease

-

A-->T (L160H)

ADA

20:43255220

rs11555566 (6.3/6.8/6.5)

Severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell- negative/NK-cell-negative due to adenosine deaminase deficiency (ADASCID)

26

Decrease

-

T-->C (K80R)

[Del count: 1; Con count: 3]

  1. *The first SNP (rs3807153) was observed in two individuals.
  2. The minor allele frequency (MAF) in percent listed in the order of European American (EA), African American (AA), and all populations (All), delimited by “/”. Prediction counts indicate the number of deleterious predictions (Del count) and conservation predictions (Con count) by six and three programs, respectively. Grantham score determines the similarity in amino acid changes: small (score < 60), intermediate (score 60–99), and large (score ≥ 100). Tertiary classification (increase, decrease, neutral) for protein stability change caused by a SNP was obtained from I-Mutant 2.0 [37], available from MSV3d [14]. Site annotations list any structurally/functionally important sites (molecule processing sites, binding sites, modification sites, etc.) where the altered amino acid residue resides. The information was retrieved from UniProt sequence feature records [13].
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ISSN: 1756-0381