X-23783398-AC-TG

Variant names:

• chrX-23783398-AC-TG
• NM_002970.4:c.47_48delACinsTG
• SAT1 p.Asp16Val

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The NM_002970.4(SAT1):​c.47_48delACinsTG​(p.Asp16Val) variant causes a missense change involving the alteration of a 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: 23)
• Consequence: SAT1 NM_002970.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 8.19
• Publications: 0 publications found

Genes affected

SAT1 (HGNC:10540): (spermidine/spermine N1-acetyltransferase 1) The protein encoded by this gene belongs to the acetyltransferase family, and is a rate-limiting enzyme in the catabolic pathway of polyamine metabolism. It catalyzes the acetylation of spermidine and spermine, and is involved in the regulation of the intracellular concentration of polyamines and their transport out of cells. Defects in this gene are associated with keratosis follicularis spinulosa decalvans (KFSD). Alternatively spliced transcripts have been found for this gene.[provided by RefSeq, Sep 2009]

SAT1-DT (HGNC:56726): (SAT1 divergent transcript)

LOC127933115 (HGNC:0):

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002970.4. 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
	SAT1	NM_002970.4	MANE Select	c.47_48delACinsTG	p.Asp16Val	missense	N/A	NP_002961.1	P21673
	SAT1	NR_027783.3		n.226_227delACinsTG		non_coding_transcript_exon	Exon 1 of 7
	LOC127933115	NM_001414725.1	MANE Select	c.*31_*32delACinsTG		downstream_gene	N/A	NP_001401654.1	A0A804HIB5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAT1	ENST00000379270.5	TSL:1 MANE Select	c.47_48delACinsTG	p.Asp16Val	missense	N/A	ENSP00000368572.4	P21673
	SAT1	ENST00000379254.5	TSL:3	c.47_48delACinsTG	p.Asp16Val	missense	N/A	ENSP00000368556.1	E9PD37
	SAT1	ENST00000379251.7	TSL:2	n.226_227delACinsTG		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 23

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

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		8.2

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: chrX-23801515;