17-31517693-ATC-GTA

Variant names:

• chr17-31517693-ATC-GTA
• NM_032932.6:c.379_381delATCinsGTA
• RAB11FIP4 p.Ile127Val

Variant summary

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

The NM_032932.6(RAB11FIP4):​c.379_381delATCinsGTA​(p.Ile127Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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: 31)
• Consequence: RAB11FIP4 NM_032932.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96
• Publications: 0 publications found

Genes affected

RAB11FIP4 (HGNC:30267): (RAB11 family interacting protein 4) The protein encoded by this gene interacts with RAB11 and is thought to be involved in bringing recycling endosome membranes to the cleavage furrow in late cytokinesis. Hypoxic conditions can lead to an upregulation of the encoded protein and enhance the metastatic potential of hepatocellular carcinoma. [provided by RefSeq, Oct 2016]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032932.6. 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
	RAB11FIP4	NM_032932.6	MANE Select	c.379_381delATCinsGTA	p.Ile127Val	missense	N/A	NP_116321.2
	RAB11FIP4	NM_001303542.3		c.73_75delATCinsGTA	p.Ile25Val	missense	N/A	NP_001290471.2	Q86YS3-2
	RAB11FIP4	NM_001346747.2		c.73_75delATCinsGTA	p.Ile25Val	missense	N/A	NP_001333676.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB11FIP4	ENST00000621161.5	TSL:1 MANE Select	c.379_381delATCinsGTA	p.Ile127Val	missense	N/A	ENSP00000482620.1	Q86YS3-1
	RAB11FIP4	ENST00000964368.1		c.379_381delATCinsGTA	p.Ile127Val	missense	N/A	ENSP00000634427.1
	RAB11FIP4	ENST00000394744.6	TSL:2	c.73_75delATCinsGTA	p.Ile25Val	missense	N/A	ENSP00000378227.2	Q86YS3-2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.0

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: chr17-29844711;