NM_015426.5(POC1A):c.889G>A (p.Val297Ile) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 17, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001767018.7

Allele description [Variation Report for NM_015426.5(POC1A):c.889G>A (p.Val297Ile)]

NM_015426.5(POC1A):c.889G>A (p.Val297Ile)

Gene:

POC1A:POC1 centriolar protein A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.2

Genomic location:

Preferred name:

NM_015426.5(POC1A):c.889G>A (p.Val297Ile)

HGVS:

NC_000003.12:g.52122471C>T
NG_032947.1:g.37220G>A
NM_001161580.2:c.889G>A
NM_001161581.2:c.775G>A
NM_015426.5:c.889G>AMANE SELECT
NP_001155052.1:p.Val297Ile
NP_001155053.1:p.Val259Ile
NP_056241.3:p.Val297Ile
NC_000003.11:g.52156487C>T
NM_015426.4:c.889G>A

Protein change:

V259I

Links:

dbSNP: rs948393275

NCBI 1000 Genomes Browser:

rs948393275

Molecular consequence:

NM_001161580.2:c.889G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001161581.2:c.775G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015426.5:c.889G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Nuclear Hormone Receptor family [Caenorhabditis elegans]
Nuclear Hormone Receptor family [Caenorhabditis elegans]
gi|17543294|ref|NP_500109.1|

Protein
Homo sapiens zinc finger DHHC-type palmitoyltransferase 23 (ZDHHC23), transcript...
Homo sapiens zinc finger DHHC-type palmitoyltransferase 23 (ZDHHC23), transcript variant 4, mRNA
gi|1677538284|ref|NM_173570.5|

Nucleotide
unnamed protein product [Homo sapiens]
unnamed protein product [Homo sapiens]
gi|194388724|dbj|BAG60330.1|

Protein
Pyxicephalus edulis isolate 1273PyxEdu 16S ribosomal RNA gene, partial sequence;...
Pyxicephalus edulis isolate 1273PyxEdu 16S ribosomal RNA gene, partial sequence; mitochondrial
gi|123286040|gb|EF107211.1|

Nucleotide
Candidatus Thioglobus sp. SCGC AG-485_F18
Candidatus Thioglobus sp. SCGC AG-485_F18
Candidatus Thioglobus sp. SCGC AG-485_F18 Genome sequencing

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001990011	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jun 3, 2019)	germline	clinical testing	Citation Link,
SCV002251147	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 17, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001990011

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jun 3, 2019)

germline

clinical testing

Citation Link,

SCV002251147

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 17, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From GeneDx, SCV001990011.2

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

Description

Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; 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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002251147.4

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

Description

This sequence change replaces valine with isoleucine at codon 297 of the POC1A protein (p.Val297Ile). This variant is present in population databases (no rsID available, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with POC1A-related conditions. ClinVar contains an entry for this variant (Variation ID: 1306065). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt POC1A protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024

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