NM_000390.4(CHM):c.534del (p.Glu179fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 13, 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:: RCV002949501.3

Allele description [Variation Report for NM_000390.4(CHM):c.534del (p.Glu179fs)]

NM_000390.4(CHM):c.534del (p.Glu179fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

Xq21.2

Genomic location:

Preferred name:

NM_000390.4(CHM):c.534del (p.Glu179fs)

HGVS:

NC_000023.11:g.85963837del
NG_009874.2:g.88730del
NM_000390.4:c.534delMANE SELECT
NM_001320959.1:c.90del
NM_001362517.1:c.90del
NM_001362518.2:c.90del
NM_001362519.1:c.90del
NP_000381.1:p.Glu179Lysfs
NP_000381.1:p.Glu179fs
NP_001307888.1:p.Glu31fs
NP_001349446.1:p.Glu31fs
NP_001349447.1:p.Glu31fs
NP_001349448.1:p.Glu31fs
LRG_699t1:c.530del
LRG_699:g.88730del
LRG_699p1:p.Glu179Lysfs
NC_000023.10:g.85218838del
NC_000023.10:g.85218842del
NM_000390.2:c.530delA

Protein change:

E179fs

Molecular consequence:

NM_000390.4:c.534del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001320959.1:c.90del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001362517.1:c.90del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001362518.2:c.90del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001362519.1:c.90del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV003286009	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 13, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9067750, 23811034, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003286009

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 13, 2022)

germline

clinical testing

PubMed (3)
[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

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

A clinical molecular genetic service for United Kingdom families with choroideraemia.

Ramsden SC, O'Grady A, Fletcher T, O'Sullivan J, Hart-Holden N, Barton SJ, Hall G, Moore AT, Webster AR, Black GC.

Eur J Med Genet. 2013 Aug;56(8):432-8. doi: 10.1016/j.ejmg.2013.06.003. Epub 2013 Jun 25.

PubMed [citation]

PMID:: 23811034

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003286009.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with CHM-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Glu179Lysfs*18) 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: Nov 10, 2024

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