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chrY-2266795-C-A

Position:

• chrY-2266795-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP5 BP4

The ENST00000711204.1(DHRSX):​c.541G>T​(p.Val181Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov:)
• Consequence: DHRSX ENST00000711204.1 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 1.25

Genes affected

DHRSX (HGNC:18399): (dehydrogenase/reductase X-linked) Predicted to enable oxidoreductase activity. Involved in positive regulation of autophagy. Located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

DHRSX_1 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PP5: Variant Y-2266795-C-A is Pathogenic according to our data. Variant chrY-2266795-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 3376532.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP4: Computational evidence support a benign effect (Cadd=20.1). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DHRSX_1	NM_145177.3_1	c.541G>T	p.Val181Phe	missense_variant	5/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DHRSX	ENST00000711204.1	c.541G>T	p.Val181Phe	missense_variant	5/7	1		ENSP00000518604.1
DHRSX	ENST00000711203.1	c.472G>T	p.Val158Phe	missense_variant	4/5	2		ENSP00000518603.1
DHRSX	ENST00000711201.1	c.340G>T	p.Val114Phe	missense_variant	5/5	2		ENSP00000518602.1
DHRSX	ENST00000711202.1	n.143G>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

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

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

Alfa AF: 0.000216 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

CONGENITAL DISORDER OF GLYCOSYLATION, TYPE 1DD Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Nov 13, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.60
CADD	Benign	20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs149133886; hg19: chrY-2134836;