NM_145691.4(ATPAF2):c.627T>G (p.Phe209Leu) AND not specified

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jul 14, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV000196158.3

Allele description [Variation Report for NM_145691.4(ATPAF2):c.627T>G (p.Phe209Leu)]

NM_145691.4(ATPAF2):c.627T>G (p.Phe209Leu)

Gene:

ATPAF2:ATP synthase mitochondrial F1 complex assembly factor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p11.2

Genomic location:

Preferred name:

NM_145691.4(ATPAF2):c.627T>G (p.Phe209Leu)

Other names:

p.F209L:TTT>TTG

HGVS:

NC_000017.11:g.18021228A>C
NG_012824.1:g.22939T>G
NM_145691.4:c.627T>GMANE SELECT
NP_663729.1:p.Phe209Leu
NC_000017.10:g.17924542A>C
NM_145691.3:c.627T>G

Protein change:

F209L

Links:

dbSNP: rs863223910

NCBI 1000 Genomes Browser:

rs863223910

Molecular consequence:

NM_145691.4:c.627T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000251164	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely benign (Dec 17, 2013)	germline	clinical testing	Citation Link,
SCV003634767	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jul 14, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000251164

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely benign
(Dec 17, 2013)

germline

clinical testing

Citation Link,

SCV003634767

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jul 14, 2022)

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

Details of each submission

From GeneDx, SCV000251164.11

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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 Ambry Genetics, SCV003634767.2

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

Description

The c.627T>G (p.F209L) alteration is located in exon 7 (coding exon 7) of the ATPAF2 gene. This alteration results from a T to G substitution at nucleotide position 627, causing the phenylalanine (F) at amino acid position 209 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

#	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: Oct 20, 2024

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