Table 3 Intronic variants and biological processes (n = 14)

SUSD5

3p22.3

This gene involves the Notch signaling pathway. Notch is the receptor in a highly conserved signaling pathway that is crucial in development and implicated in malignant transformation [42].

MACROD2

20p12.1

MACROD2 acts as a haploinsufficient caretaker of the tumor suppressor gene. Loss of function mutations of this gene promote chromosome instability, resulting in cancer evolution [43].

RPTOR

17q25.3

The class I phosphoinositide 3-kinase (PI3K)– mechanistic target of rapamycin complex 1(mTORC1) signaling network directs cellular metabolism and growth, which is implicated in diverse pathologies, including cancer, when dysregulated [44].

ARHGAP24

4q21.23

As key regulators of cytoskeletal dynamics, Rho GTPases activated by ARHGAP24 coordinate a wide range of cellular processes, including cell cycle progression and cell migration, which enables cancer cells to invade the stroma surrounding the primary tumor [45].

PPFIBP2

11p15.4

PPFIBP2 is considered to promote tumor suppressor properties. Germline loss-of-function mutations of PPFIBP2 have been associated with shorter survival in prostate cancer [46].

SPTBN4

19q13.2

This gene involves MARK1/MARK3 signaling. This kinase pathway is a central signaling module that participates in physiological and pathological processes like cancer [47].

SNCAIP

5q23.2

RNA expression of SNCA and SNCAIP was observed to have a close relationship with medulloblastoma, a brain tumor which has been reported to be related with various tumors [48].

NEK6

9q33.3

NEK6 interacts with STAT3, which is an oncogenic transcription factor. It phosphorylates STAT3 on Ser⁷²⁷, which is important for transcriptional activation [49].

DPF3

14q24.2

This gene is a component of the BAF chromatin remodeling complex (ATP remodeling complex). BAF complex subunits are frequently altered in cancer with up to 20% of human cancers [50].

ZNF804B

7q21.13

Differential expression levels of ZNF proteins in different cancer types are regulated by cancer-related miRNA [51].

CAMSAP1

9q34.3

CAMSAP1 mutation can activate anti-tumor immunity, mediate tumor cell apoptosis, and improve platinum drug sensitivity [52].

C2CD2

21q22.3

C2CD2 mutations were associated with a higher incidence of colorectal adenomas. C2CD2 up-regulation lead to cytosolic Ca²⁺ increase involved in the regulation of apoptosis [53].

GRIP1

12q14.3

The PKA-stimulated degradation of GRIP1 leads to changes in the expression of a subset of genes regulated by estrogen receptor-α in MCF-7 breast cancer cells [54].

TBC1D16

17q25.3

The TBC domain family is implicated in various cellular events contributing to initiation and development of different cancers [55].