rs781797236

Variant names:

• chrX-154428787-TGGCGGCGGCGGC-T
• rs781797236
• NM_001183.6:c.105_116delGGCGGCGGCGGC

Your query was ambiguous. Multiple possible variants found:

• chrX-154428787-TGGCGGCGGCGGC-T
• chrX-154428787-TGGCGGCGGCGGC-TGGC
• chrX-154428787-TGGCGGCGGCGGC-TGGCGGC
• chrX-154428787-TGGCGGCGGCGGC-TGGCGGCGGC
• chrX-154428787-TGGCGGCGGCGGC-TGGCGGCGGCGGCGGC
• chrX-154428787-TGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGC
• chrX-154428787-TGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGC
• chrX-154428787-TGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGC
• chrX-154428787-TGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGC
• chrX-154428787-TGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001183.6(ATP6AP1):​c.105_116delGGCGGCGGCGGC​(p.Ala36_Ala39del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 21)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: ATP6AP1 NM_001183.6 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

Genes affected

ATP6AP1 (HGNC:868): (ATPase H+ transporting accessory protein 1) This gene encodes a component of a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. Vacuolar ATPase (V-ATPase) is comprised of a cytosolic V1 (site of the ATP catalytic site) and a transmembrane V0 domain. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, and receptor-mediated endocytosis. The encoded protein of this gene may assist in the V-ATPase-mediated acidification of neuroendocrine secretory granules. This protein may also play a role in early development. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP6AP1	NM_001183.6	c.105_116delGGCGGCGGCGGC	p.Ala36_Ala39del	disruptive_inframe_deletion	Exon 1 of 10	ENST00000369762.7	NP_001174.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP6AP1	ENST00000369762.7	c.105_116delGGCGGCGGCGGC	p.Ala36_Ala39del	disruptive_inframe_deletion	Exon 1 of 10	1	NM_001183.6	ENSP00000358777.2

Frequencies

GnomAD3 genomes Cov.: 21

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1012550 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 325978

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 21

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs781797236; hg19: chrX-153657133;