NM_001015877.2(PHF6):c.176A>G (p.Asn59Ser) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 30, 2015
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:: RCV000497949.1

Allele description [Variation Report for NM_001015877.2(PHF6):c.176A>G (p.Asn59Ser)]

NM_001015877.2(PHF6):c.176A>G (p.Asn59Ser)

Gene:

PHF6:PHD finger protein 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq26.2

Genomic location:

Preferred name:

NM_001015877.2(PHF6):c.176A>G (p.Asn59Ser)

HGVS:

NC_000023.11:g.134378042A>G
NG_008886.1:g.9731A>G
NM_001015877.2:c.176A>GMANE SELECT
NM_032335.3:c.176A>G
NM_032458.3:c.176A>G
NP_001015877.1:p.Asn59Ser
NP_115711.2:p.Asn59Ser
NP_115834.1:p.Asn59Ser
LRG_629t2:c.176A>G
LRG_629:g.9731A>G
LRG_629p2:p.Asn59Ser
NC_000023.10:g.133512072A>G
NM_032458.2:c.176A>G

Protein change:

N59S

Links:

dbSNP: rs202007952

Molecular consequence:

NM_001015877.2:c.176A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_032335.3:c.176A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_032458.3:c.176A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000589452	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Jul 30, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000589452

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Jul 30, 2015)

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, SCV000589452.3

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

Description

The N59S variant has not been published as a pathogenic variant, nor has it been reported as a benign polymorphism to our knowledge. It was not observed with any significant frequency in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project. The N59S variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position where amino acids with similar properties to Asparagine are tolerated across species, and Serine is observed at this position in evolution. However, in silico analysis is inconsistent in its predictions as to whether or not the N59S variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

#	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: Apr 12, 2026

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