NM_177939.3(P4HTM):c.659G>A (p.Trp220Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 11, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001653151.2

Allele description [Variation Report for NM_177939.3(P4HTM):c.659G>A (p.Trp220Ter)]

NM_177939.3(P4HTM):c.659G>A (p.Trp220Ter)

Gene:

P4HTM:prolyl 4-hydroxylase, transmembrane [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.31

Genomic location:

Preferred name:

NM_177939.3(P4HTM):c.659G>A (p.Trp220Ter)

HGVS:

NC_000003.12:g.49002531G>A
NG_029915.1:g.328G>A
NM_177938.2:c.659G>A
NM_177939.3:c.659G>AMANE SELECT
NP_808807.2:p.Trp220Ter
NP_808808.1:p.Trp220Ter
NC_000003.11:g.49039964G>A

Protein change:

W220*

Links:

dbSNP: rs1339145374

NCBI 1000 Genomes Browser:

rs1339145374

Molecular consequence:

NM_177938.2:c.659G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_177939.3:c.659G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens
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RefSeq annotation of the human reference genome assembly

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001871352	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 11, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001871352

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 11, 2021)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV001871352.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

ClinVar

Relating variation to medicine