NM_000390.4(CHM):c.1603G>T (p.Glu535Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 7, 2022
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:: RCV003041458.3

Allele description [Variation Report for NM_000390.4(CHM):c.1603G>T (p.Glu535Ter)]

NM_000390.4(CHM):c.1603G>T (p.Glu535Ter)

Gene:

CHM:CHM Rab escort protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq21.2

Genomic location:

Preferred name:

NM_000390.4(CHM):c.1603G>T (p.Glu535Ter)

HGVS:

NC_000023.11:g.85878971C>A
NG_009874.2:g.173592G>T
NM_000390.4:c.1603G>TMANE SELECT
NM_001320959.1:c.1159G>T
NM_001362517.1:c.1159G>T
NM_001362518.2:c.1159G>T
NM_001362519.1:c.1159G>T
NP_000381.1:p.Glu535Ter
NP_000381.1:p.Glu535Ter
NP_001307888.1:p.Glu387Ter
NP_001349446.1:p.Glu387Ter
NP_001349447.1:p.Glu387Ter
NP_001349448.1:p.Glu387Ter
LRG_699t1:c.1603G>T
LRG_699:g.173592G>T
LRG_699p1:p.Glu535Ter
NC_000023.10:g.85133976C>A
NM_000390.2:c.1603G>T

Protein change:

E387*

Molecular consequence:

NM_000390.4:c.1603G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001320959.1:c.1159G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001362517.1:c.1159G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001362518.2:c.1159G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001362519.1:c.1159G>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV003445090	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 7, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 12203991, 9067750, 23811034, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003445090

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 7, 2022)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Citations

PubMed

Mutational analysis of patients with the diagnosis of choroideremia.

McTaggart KE, Tran M, Mah DY, Lai SW, Nesslinger NJ, MacDonald IM.

Hum Mutat. 2002 Sep;20(3):189-96.

PubMed [citation]

PMID:: 12203991

Molecular basis of choroideremia (CHM): mutations involving the Rab escort protein-1 (REP-1) gene.

van den Hurk JA, Schwartz M, van Bokhoven H, van de Pol TJ, Bogerd L, Pinckers AJ, Bleeker-Wagemakers EM, Pawlowitzki IH, Rüther K, Ropers HH, Cremers FP.

Hum Mutat. 1997;9(2):110-7. Review.

PubMed [citation]

PMID:: 9067750

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003445090.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This premature translational stop signal has been observed in individual(s) with choroideremia (PMID: 12203991). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Glu535*) in the CHM gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CHM are known to be pathogenic (PMID: 9067750, 23811034).

#	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: Sep 29, 2024

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