GeneBe

rs781797236

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

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. 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: 21)
Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control

Consequence

ATP6AP1
NM_001183.6 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.270

Publications

3 publications found
Variant links:
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]
ATP6AP1-DT (HGNC:25138): (ATP6AP1 divergent transcript)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_001183.6

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001183.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ATP6AP1
NM_001183.6
MANE Select
c.105_116delGGCGGCGGCGGCp.Ala36_Ala39del
disruptive_inframe_deletion
Exon 1 of 10NP_001174.2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ATP6AP1
ENST00000369762.7
TSL:1 MANE Select
c.105_116delGGCGGCGGCGGCp.Ala36_Ala39del
disruptive_inframe_deletion
Exon 1 of 10ENSP00000358777.2Q15904
ATP6AP1
ENST00000945275.1
c.105_116delGGCGGCGGCGGCp.Ala36_Ala39del
disruptive_inframe_deletion
Exon 1 of 11ENSP00000615334.1
ATP6AP1
ENST00000862438.1
c.105_116delGGCGGCGGCGGCp.Ala36_Ala39del
disruptive_inframe_deletion
Exon 1 of 10ENSP00000532497.1

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
African (AFR)
AF:
0.00
AC:
0
AN:
20805
American (AMR)
AF:
0.00
AC:
0
AN:
22652
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
16951
East Asian (EAS)
AF:
0.00
AC:
0
AN:
24117
South Asian (SAS)
AF:
0.00
AC:
0
AN:
46153
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
28515
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3622
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
806972
Other (OTH)
AF:
0.00
AC:
0
AN:
42763
GnomAD4 genome
Cov.:
21
Alfa
AF:
0.00
Hom.:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.27

Splicing

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

Publications

Other links and lift over

dbSNP: rs781797236; hg19: chrX-153657133; API