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Table 2 Analyzed genes and variants with their involvement in blood-related functions and cancer

From: Driving mosaicism: somatic variants in reference population databases and effect on variant interpretation in rare genetic disease

Gene**

AD condition

Variant***

Variant type

Allele count (< 35% of reads)

COSMIC

ExAC

gnomAD

AA mutation

Confirmed somatic

No. of samples

Samples being ‘hematopoietic and lymphoid’

ASXL1 *â–²

Bohring–Opitz syndrome

NM_015338.5:c.1210C>Tâ–º

Nonsense

3

3

p.R404*

Yes

10

90.0%

  

NM_015338.5:c.2893C>Tâ–º

Nonsense

1

2

p.R965*

Yes

17

70.6%

  

NM_015338.5:c.1117C>Tâ–º

Nonsense

0

2

–

–

–

–

BRAF*∆

Cardio-facio-cutaneous

NM_004333.5:c.1799T>Aâ–º

Missense

1

2

p.V600E

Yes

29,274

3.0%

 

syndrome

NM_004333.5:c.1406G>A

Missense

1

0

p.G469E

Yes

28

0.0%

CBL*

Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia

NM_005188.3:c.1186T>C

Missense

1

0

p.C396R

Yes

13

100.0%

  

NM_005188.3:c.1259G>Aâ–º

Missense

2

2

p.R420Q

Yes

27

77.8%

  

NM_005188.3:c.1111T>Câ–º

Missense

1

2

p.Y371H

Yes

30

96.7%

DNMT3A*

Tatton–Brown–Rahman syndrome

NM_022552.5:c.2312G>Aâ–º

Missense

3

2

p.R771Q

Yes

8

50.0%

  

NM_022552.5:c.2644C>Tâ–º

Missense

4

3

p.R882C

Yes

398

98.5%

  

NM_022552.5:c.2536C>T

Nonsense

1

0

p.Q846*

No

1

100.0%

FGFR3▲∆

LADD syndrome/Thanatophoric dysplasia, type I

NM_000142.5:c.1537G>A

Missense

1

0

–

–

–

–

  

NM_000142.5:c.746C>Gâ–º

Missense

1

0

p.S249C

Yes

1,525

0.0%

IDH2*∆

D-2-hydroxyglutaric aciduria 2

NM_001289910.1:c.263G>A

Missense

4

3

–

–

–

–

KRAS*∆

Noonan syndrome 3/RAS-associated autoimmune leukoproliferative disorder

NM_004985.4:c.40G>Aâ–º

Missense

1

0

p.V14I

Yes

34

14.71%

  

NM_004985.4:c.35G>Aâ–º

Missense

1

1

p.G12D

Yes

15,834

1.67%

PTPN11*

Noonan syndrome 1

NM_002834.5:c.1471C>Tâ–º

Missense

1

NA

–

–

–

–

  

NM_002834.5:c.794G>Aâ–º

Missense

1

0

p.R265Q

Yes

4

100.0%

  

NM_002834.5:c.188A>Gâ–º

Missense

0

1

p.Y63C

No

4

100.0%

SETBP1

Schinzel–Giedion midface retraction syndrome

NM_015559.3:c.2608G>Aâ–º

Missense

2

1

p.G870S

Yes

72

98.61%

  1. A total of 16 variants (80.0% of variants reported here) residing in genes with good evidence of somatic mosaicism were also present in the Catalogue of Somatic Mutations in Cancer (COSMIC; info obtained on February 4, 2021). Across the genes, the variants were found in 1 to 29,274 samples. It is expected that the more frequent a mutation is in cancer samples, the higher the chance is that it is a driver mutation (the mechanism that makes those cells and the variants they carry more abundant in blood). A driver mutation is by definition a genetic change that gives an advantage to the cell. The advantage enables the cell to grow and proliferate better than other cells, which is a hallmark in cancer
  2. AA, amino acid; AD, autosomal dominant; ASXL1, ASXL transcriptional regulator 1; BRAF, B-Raf proto-oncogene, serine/threonine kinase; CBL, Cbl proto-oncogene; COSMIC, Catalogue of Somatic Mutations in Cancer; DNMT3A, DNA methyltransferase 3 alpha; FGFR3, fibroblast growth factor receptor 3; IDH2, isocitrate dehydrogenase (NADP(+)) 2;; LADD, Lacrimo-auriculo-dento-digital; KRAS, KRAS proto-oncogene, GTPase; PTPN11, protein tyrosine phosphatase non-receptor type 11
  3. â–²Evidence of somatic mosaicism involving the germline reported by Erickson [39] or Bedoukian et al.[30]
  4. ∆Genes involved in stem cell and/or cell population proliferation
  5. â–ºVariant reported to affect or probably affect function based on Leiden Open Variation Database (LOVD; hg19/GRCh37) version 3.0 [40]
  6. *Genes with evidence of mosaicism that overlap with the list of 156 hematopoietic genes provided by Jaiswal et al. [13] in their Additional file 1: Table S2 (n = 7)
  7. **A gene shows good evidence of mosaicism when at least two alleles show signs of somatic origin (allelic imbalance)
  8. ***Rare disease- and/or cancer-related known pathogenic or likely pathogenic variants (in ClinVar and/or COSMIC)