NM_020863.4(ZFAT):c.1409C>G (p.Ser470Cys) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Nov 1, 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:: RCV003437202.11

Allele description [Variation Report for NM_020863.4(ZFAT):c.1409C>G (p.Ser470Cys)]

NM_020863.4(ZFAT):c.1409C>G (p.Ser470Cys)

Genes:

LOC130001238:ATAC-STARR-seq lymphoblastoid active region 28015 [Gene]
ZFAT:zinc finger and AT-hook domain containing [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q24.22

Genomic location:

Preferred name:

NM_020863.4(ZFAT):c.1409C>G (p.Ser470Cys)

HGVS:

NC_000008.11:g.134602310G>C
NG_016356.2:g.115740C>G
NM_001029939.4:c.1373C>G
NM_001167583.3:c.1373C>G
NM_001174157.2:c.1223C>G
NM_001174158.2:c.1373C>G
NM_001289394.2:c.1373C>G
NM_020863.4:c.1409C>GMANE SELECT
NP_001025110.2:p.Ser458Cys
NP_001161055.1:p.Ser458Cys
NP_001167628.1:p.Ser408Cys
NP_001167629.1:p.Ser458Cys
NP_001276323.1:p.Ser458Cys
NP_065914.2:p.Ser470Cys
NC_000008.10:g.135614553G>C
NG_016356.1:g.115740C>G
NM_001029939.3:c.1373C>G
NR_110323.2:n.1577C>G

Protein change:

S408C

Links:

dbSNP: rs112892337

NCBI 1000 Genomes Browser:

rs112892337

Molecular consequence:

NM_001029939.4:c.1373C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001167583.3:c.1373C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001174157.2:c.1223C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001174158.2:c.1373C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001289394.2:c.1373C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_020863.4:c.1409C>G - missense variant - [Sequence Ontology: SO:0001583]
NR_110323.2:n.1577C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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
SCV004163283	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Nov 1, 2022)	germline	clinical testing	Citation Link,
SCV005196131	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004163283

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Nov 1, 2022)

germline

clinical testing

Citation Link,

SCV005196131

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

germline

not provided

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	1	not provided	not provided	not provided	not provided	clinical testing, not provided

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV004163283.10

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

Description

ZFAT: BS2

#	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		1	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005196131.1

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

#	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: Oct 20, 2024

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