NM_024956.4(TMEM62):c.1588A>G (p.Ile530Val) AND not specified

Germline classification:: Likely benign (1 submission)
Last evaluated:: Nov 14, 2023
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:: RCV004470399.1

Allele description [Variation Report for NM_024956.4(TMEM62):c.1588A>G (p.Ile530Val)]

NM_024956.4(TMEM62):c.1588A>G (p.Ile530Val)

Gene:

TMEM62:transmembrane protein 62 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q15.2

Genomic location:

Preferred name:

NM_024956.4(TMEM62):c.1588A>G (p.Ile530Val)

HGVS:

NC_000015.10:g.43181282A>G
NM_001347004.1:c.1198A>G
NM_001347005.2:c.1198A>G
NM_001347006.2:c.1198A>G
NM_001347007.2:c.1198A>G
NM_001347008.1:c.1192A>G
NM_001347009.1:c.1192A>G
NM_001347010.2:c.1192A>G
NM_001347011.2:c.1192A>G
NM_001347012.2:c.1192A>G
NM_001347013.2:c.1192A>G
NM_001347014.1:c.1093A>G
NM_001347015.2:c.1093A>G
NM_001347016.2:c.1093A>G
NM_001347017.2:c.1087A>G
NM_001347018.2:c.1087A>G
NM_001347019.1:c.973A>G
NM_001347020.2:c.973A>G
NM_001347021.2:c.973A>G
NM_001347023.2:c.973A>G
NM_001347024.1:c.868A>G
NM_001347025.1:c.868A>G
NM_001347026.2:c.868A>G
NM_001347027.2:c.868A>G
NM_001347028.2:c.868A>G
NM_001347029.2:c.868A>G
NM_001347030.1:c.826A>G
NM_001347031.2:c.1216A>G
NM_001347032.2:c.1483A>G
NM_001347033.2:c.1321A>G
NM_001347034.2:c.859A>G
NM_024956.4:c.1588A>GMANE SELECT
NP_001333933.1:p.Ile400Val
NP_001333934.1:p.Ile400Val
NP_001333935.1:p.Ile400Val
NP_001333936.1:p.Ile400Val
NP_001333937.1:p.Ile398Val
NP_001333938.1:p.Ile398Val
NP_001333939.1:p.Ile398Val
NP_001333940.1:p.Ile398Val
NP_001333941.1:p.Ile398Val
NP_001333942.1:p.Ile398Val
NP_001333943.1:p.Ile365Val
NP_001333944.1:p.Ile365Val
NP_001333945.1:p.Ile365Val
NP_001333946.1:p.Ile363Val
NP_001333947.1:p.Ile363Val
NP_001333948.1:p.Ile325Val
NP_001333949.1:p.Ile325Val
NP_001333950.1:p.Ile325Val
NP_001333952.1:p.Ile325Val
NP_001333953.1:p.Ile290Val
NP_001333954.1:p.Ile290Val
NP_001333955.1:p.Ile290Val
NP_001333956.1:p.Ile290Val
NP_001333957.1:p.Ile290Val
NP_001333958.1:p.Ile290Val
NP_001333959.1:p.Ile276Val
NP_001333960.1:p.Ile406Val
NP_001333961.1:p.Ile495Val
NP_001333962.1:p.Ile441Val
NP_001333963.1:p.Ile287Val
NP_079232.3:p.Ile530Val
NC_000015.9:g.43473480A>G
NM_024956.3:c.1588A>G
NR_144541.1:n.1512A>G
NR_144542.2:n.1621A>G
NR_144543.2:n.1653A>G
NR_144544.2:n.1575A>G

Protein change:

I276V

Molecular consequence:

NM_001347004.1:c.1198A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347005.2:c.1198A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347006.2:c.1198A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347007.2:c.1198A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347008.1:c.1192A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347009.1:c.1192A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347010.2:c.1192A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347011.2:c.1192A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347012.2:c.1192A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347013.2:c.1192A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347014.1:c.1093A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347015.2:c.1093A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347016.2:c.1093A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347017.2:c.1087A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347018.2:c.1087A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347019.1:c.973A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347020.2:c.973A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347021.2:c.973A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347023.2:c.973A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347024.1:c.868A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347025.1:c.868A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347026.2:c.868A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347027.2:c.868A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347028.2:c.868A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347029.2:c.868A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347030.1:c.826A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347031.2:c.1216A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347032.2:c.1483A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347033.2:c.1321A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347034.2:c.859A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_024956.4:c.1588A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_144541.1:n.1512A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_144542.2:n.1621A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_144543.2:n.1653A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_144544.2:n.1575A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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PREDICTED: Homo sapiens lysine demethylase 8 (KDM8), transcript variant X3, mRNA
PREDICTED: Homo sapiens lysine demethylase 8 (KDM8), transcript variant X3, mRNA
gi|2217307513|ref|XM_047434655.1|

Nucleotide
PREDICTED: Homo sapiens interleukin 27 (IL27), transcript variant X1, mRNA
PREDICTED: Homo sapiens interleukin 27 (IL27), transcript variant X1, mRNA
gi|2462548316|ref|XM_054379989.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004967227	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Nov 14, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004967227

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Nov 14, 2023)

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

Details of each submission

From Ambry Genetics, SCV004967227.1

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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: May 7, 2024

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