NM_206538.4(EMC10):c.70C>T (p.Arg24Ter) AND EMC10-related disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 9, 2024
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV003892179.2

Allele description [Variation Report for NM_206538.4(EMC10):c.70C>T (p.Arg24Ter)]

NM_206538.4(EMC10):c.70C>T (p.Arg24Ter)

Genes:

EMC10:ER membrane protein complex subunit 10 [Gene - OMIM - HGNC]
GARIN5A:golgi associated RAB2 interactor 5A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.33

Genomic location:

Preferred name:

NM_206538.4(EMC10):c.70C>T (p.Arg24Ter)

HGVS:

NC_000019.10:g.50476614C>T
NG_141889.1:g.570C>T
NG_141889.2:g.570C>T
NM_001308429.2:c.-226G>AMANE SELECT
NM_138411.3:c.-226G>A
NM_175063.6:c.70C>T
NM_206538.4:c.70C>TMANE SELECT
NP_778233.4:p.Arg24Ter
NP_996261.1:p.Arg24Ter
NC_000019.9:g.50979871C>T
NM_206538.3:c.70C>T

Protein change:

R24*

Links:

dbSNP: rs953380956

NCBI 1000 Genomes Browser:

rs953380956

Molecular consequence:

NM_001308429.2:c.-226G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_138411.3:c.-226G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_175063.6:c.70C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_206538.4:c.70C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: EMC10-related disorder
Synonyms:: EMC10-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004711482	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Likely pathogenic (Feb 9, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004711482

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Likely pathogenic
(Feb 9, 2024)

germline

clinical testing

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 PreventionGenetics, part of Exact Sciences, SCV004711482.2

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

Description

The EMC10 c.70C>T variant is predicted to result in premature protein termination (p.Arg24*). To our knowledge this variant has not been reported in the literature. This variant is reported in 1 out ~171,000 of alleles in individuals in gnomAD (Other Population). Nonsense variants in EMC10 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

#	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 13, 2024

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