rs71402581

Variant names:

• chr16-5027392-GATGGGAGGAGGGAG-GAT
• NM_016256.4:c.1175-27_1175-16delCTCCCTCCTCCC

Your query was ambiguous. Multiple possible variants found:

• chr16-5027394-TGGGAGGAGGGAGGA-T
• chr16-5027394-TGGGAGGAGGGAGGA-TGGGAGGA
• chr16-5027394-TGGGAGGAGGGAGGA-TGGGAGGAGGGAGGAGGGAGGA
• chr16-5027394-TGGGAGGAGGGAGGA-TGGGAGGAGGGAGGAGGGAGGAGGGAGGA

Variant summary

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

The NM_016256.4(NAGPA):​c.1175-27_1175-16delCTCCCTCCTCCC variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, 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.

• Frequency: Genomes: not found (cov: 0)
• Consequence: NAGPA NM_016256.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 0 publications found

Genes affected

NAGPA (HGNC:17378): (N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase) Hydrolases are transported to lysosomes after binding to mannose 6-phosphate receptors in the trans-Golgi network. This gene encodes the enzyme that catalyzes the second step in the formation of the mannose 6-phosphate recognition marker on lysosomal hydrolases. Commonly known as 'uncovering enzyme' or UCE, this enzyme removes N-acetyl-D-glucosamine (GlcNAc) residues from GlcNAc-alpha-P-mannose moieties and thereby produces the recognition marker. The encoded preproprotein is proteolytically processed by furin to generate the mature enzyme, a homotetramer of two disulfide-linked homodimers. Mutations in this gene are associated with developmental stuttering in human patients. [provided by RefSeq, Oct 2015]

ENSG00000267072 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016256.4. 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
	NAGPA	NM_016256.4	MANE Select	c.1175-27_1175-16delCTCCCTCCTCCC		intron	N/A	NP_057340.2	Q9UK23-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAGPA	ENST00000312251.8	TSL:1 MANE Select	c.1175-27_1175-16delCTCCCTCCTCCC		intron	N/A	ENSP00000310998.3	Q9UK23-1
	NAGPA	ENST00000948540.1		c.1277-27_1277-16delCTCCCTCCTCCC		intron	N/A	ENSP00000618599.1
	NAGPA	ENST00000948538.1		c.1175-27_1175-16delCTCCCTCCTCCC		intron	N/A	ENSP00000618597.1

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.2

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: chr16-5077393;