rs878854357

Positions:

• chrX-151403610-TCTTTGTTTA-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

The NM_001017980.4(VMA21):​c.54-16_54-8delGTTTACTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 24)
• Consequence: VMA21 NM_001017980.4 splice_region, intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 3.11

Genes affected

VMA21 (HGNC:22082): (vacuolar ATPase assembly factor VMA21) This gene encodes a chaperone for assembly of lysosomal vacuolar ATPase.[provided by RefSeq, Jul 2012]

VMA21 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-151403610-TCTTTGTTTA-T is Pathogenic according to our data. Variant chrX-151403610-TCTTTGTTTA-T is described in ClinVar as [Pathogenic]. Clinvar id is 208806.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-151403610-TCTTTGTTTA-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VMA21	NM_001017980.4	c.54-16_54-8delGTTTACTTT		splice_region_variant, intron_variant		ENST00000330374.7	NP_001017980.1
VMA21	NM_001363810.1	c.219-16_219-8delGTTTACTTT		splice_region_variant, intron_variant			NP_001350739.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VMA21	ENST00000330374.7	c.54-16_54-8delGTTTACTTT		splice_region_variant, intron_variant		1	NM_001017980.4	ENSP00000333255.6
VMA21	ENST00000370361.5	c.219-16_219-8delGTTTACTTT		splice_region_variant, intron_variant		5		ENSP00000359386.1
VMA21	ENST00000477649.1	n.134-16_134-8delGTTTACTTT		splice_region_variant, intron_variant		3

Frequencies

GnomAD3 genomes Cov.: 24

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

GnomAD4 genome Cov.: 24

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

X-linked myopathy with excessive autophagy Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 01, 2015

- -

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: rs878854357; hg19: chrX-150572082;