rs587776676

Variant names:

• chr4-174518054-GGTCTACAAC-TG
• rs587776676
• NM_000860.6:c.232_241delGTTGTAGACCinsCA

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_000860.6(HPGD):​c.232_241delGTTGTAGACCinsCA​(p.Val78GlnfsTer11) variant causes a frameshift, missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: HPGD NM_000860.6 frameshift, missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 6.25
• Publications: 1 publications found

Genes affected

HPGD (HGNC:5154): (15-hydroxyprostaglandin dehydrogenase) This gene encodes a member of the short-chain nonmetalloenzyme alcohol dehydrogenase protein family. The encoded enzyme is responsible for the metabolism of prostaglandins, which function in a variety of physiologic and cellular processes such as inflammation. Mutations in this gene result in primary autosomal recessive hypertrophic osteoarthropathy and cranioosteoarthropathy. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

HPGD Gene-Disease associations (from GenCC):

• hypertrophic osteoarthropathy, primary, autosomal recessive, 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• cranio-osteoarthropathy

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• pachydermoperiostosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• isolated congenital digital clubbing

  Inheritance: Unknown, AD, AR Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics

ACMG classification

Our verdict: Pathogenic. The variant received 11 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 4-174518054-GGTCTACAAC-TG is Pathogenic according to our data. Variant chr4-174518054-GGTCTACAAC-TG is described in ClinVar as Pathogenic. ClinVar VariationId is 7918.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000860.6. 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
	HPGD	NM_000860.6	MANE Select	c.232_241delGTTGTAGACCinsCA	p.Val78GlnfsTer11	frameshift missense	Exon 3 of 7	NP_000851.2
	HPGD	NM_001145816.3		c.232_241delGTTGTAGACCinsCA	p.Val78GlnfsTer11	frameshift missense	Exon 3 of 6	NP_001139288.1	P15428-2
	HPGD	NM_001363574.2		c.232_241delGTTGTAGACCinsCA	p.Val78GlnfsTer11	frameshift missense	Exon 3 of 5	NP_001350503.1	E9PBZ2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HPGD	ENST00000296522.11	TSL:1 MANE Select	c.232_241delGTTGTAGACCinsCA	p.Val78GlnfsTer11	frameshift missense	Exon 3 of 7	ENSP00000296522.6	P15428-1
	HPGD	ENST00000296521.11	TSL:1	c.232_241delGTTGTAGACCinsCA	p.Val78GlnfsTer11	frameshift missense	Exon 3 of 6	ENSP00000296521.7	P15428-2
	HPGD	ENST00000542498.5	TSL:1	c.232_241delGTTGTAGACCinsCA	p.Val78GlnfsTer11	frameshift missense	Exon 3 of 5	ENSP00000443644.1	P15428-4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
1	-	-	Hypertrophic osteoarthropathy, primary, autosomal recessive, 1 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.3
Mutation Taster		=1/199	disease causing (fs/PTC)

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

dbSNP: rs587776676; hg19: chr4-175439205;