chr1-205569085-CGC-TTA

Variant names:

• chr1-205569085-CGC-TTA
• NM_181644.5:c.16_18delCGCinsTTA
• SLC60A1 p.Arg6Leu

Variant summary

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

The NM_181644.5(SLC60A1):​c.16_18delCGCinsTTA​(p.Arg6Leu) 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. R6H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: SLC60A1 NM_181644.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.50
• Publications: 0 publications found

Genes affected

SLC60A1 (HGNC:25433): (major facilitator superfamily domain containing 4A) Predicted to enable glucose transmembrane transporter activity. Predicted to be involved in glucose transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

MFSD4A-AS1 (HGNC:):

SLC60A1-AS1 (HGNC:27632): (MFSD4A antisense RNA 1)

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181644.5. 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
	SLC60A1	NM_181644.5	MANE Select	c.16_18delCGCinsTTA	p.Arg6Leu	missense	N/A	NP_857595.3
	SLC60A1-AS1	NR_027086.2		n.177+42_177+44delGCGinsTAA		intron	N/A
	SLC60A1-AS1	NR_152721.1		n.177+42_177+44delGCGinsTAA		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFSD4A	ENST00000367147.9	TSL:1 MANE Select	c.16_18delCGCinsTTA	p.Arg6Leu	missense	N/A	ENSP00000356115.4	Q8N468-1
	MFSD4A	ENST00000873628.1		c.16_18delCGCinsTTA	p.Arg6Leu	missense	N/A	ENSP00000543687.1
	MFSD4A	ENST00000873627.1		c.16_18delCGCinsTTA	p.Arg6Leu	missense	N/A	ENSP00000543686.1

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		5.5

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: chr1-205538213;