1-178300103-GGC-TCA

Variant names:

• chr1-178300103-GGC-TCA
• NM_170692.4:c.442_444delGGCinsTCA
• RASAL2 p.Gly148Ser

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_170692.4(RASAL2):​c.442_444delGGCinsTCA​(p.Gly148Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RASAL2 NM_170692.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.09
• Publications: 0 publications found

Genes affected

RASAL2 (HGNC:9874): (RAS protein activator like 2) This gene encodes a protein that contains the GAP-related domain (GRD), a characteristic domain of GTPase-activating proteins (GAPs). GAPs function as activators of Ras superfamily of small GTPases. The protein encoded by this gene is able to complement the defective RasGAP function in a yeast system. Two alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_170692.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RASAL2	NM_170692.4	MANE Select	c.442_444delGGCinsTCA	p.Gly148Ser	missense	N/A	NP_733793.2	Q9UJF2-2
	RASAL2	NM_001437625.1		c.442_444delGGCinsTCA	p.Gly148Ser	missense	N/A	NP_001424554.1
	RASAL2	NM_001437626.1		c.442_444delGGCinsTCA	p.Gly148Ser	missense	N/A	NP_001424555.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RASAL2	ENST00000367649.8	TSL:1 MANE Select	c.442_444delGGCinsTCA	p.Gly148Ser	missense	N/A	ENSP00000356621.3	Q9UJF2-2
	RASAL2	ENST00000696605.1		c.829_831delGGCinsTCA	p.Gly277Ser	missense	N/A	ENSP00000512749.1	A0A8Q3SIU1
	RASAL2	ENST00000902905.1		c.442_444delGGCinsTCA	p.Gly148Ser	missense	N/A	ENSP00000572964.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr1-178269238;