17-5032981-GTC-ATT

Variant names:

• chr17-5032981-GTC-ATT
• NM_017986.4:c.1321_1323delGACinsAAT
• SLC52A1 p.Asp441Asn

Variant summary

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

The NM_017986.4(SLC52A1):​c.1321_1323delGACinsAAT​(p.Asp441Asn) 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. D441H) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: SLC52A1 NM_017986.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.963
• Publications: 0 publications found

Genes affected

SLC52A1 (HGNC:30225): (solute carrier family 52 member 1) Biological redox reactions require electron donors and acceptor. Vitamin B2 is the source for the flavin in flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) which are common redox reagents. This gene encodes a member of the riboflavin (vitamin B2) transporter family. Haploinsufficiency of this protein can cause maternal riboflavin deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2013]

SLC52A1 Gene-Disease associations (from GenCC):

• ariboflavinosis

  Inheritance: AD, Unknown Classification: MODERATE, LIMITED Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)
• maternal riboflavin deficiency

  Inheritance: AD Classification: MODERATE, SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, ClinGen, Orphanet

LOC105371501 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017986.4. 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
	SLC52A1	NM_017986.4	MANE Select	c.1321_1323delGACinsAAT	p.Asp441Asn	missense	N/A	NP_060456.3
	SLC52A1	NM_001104577.2		c.1321_1323delGACinsAAT	p.Asp441Asn	missense	N/A	NP_001098047.1	Q9NWF4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC52A1	ENST00000254853.10	TSL:1 MANE Select	c.1321_1323delGACinsAAT	p.Asp441Asn	missense	N/A	ENSP00000254853.5	Q9NWF4-1
	SLC52A1	ENST00000424747.1	TSL:1	c.1321_1323delGACinsAAT	p.Asp441Asn	missense	N/A	ENSP00000399979.1	Q9NWF4-1
	SLC52A1	ENST00000894338.1		c.1321_1323delGACinsAAT	p.Asp441Asn	missense	N/A	ENSP00000564397.1

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		0.96

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: chr17-4936276;