NM_000390.4(CHM):c.1595C>A (p.Thr532Asn) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 17, 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:: RCV001341772.5

Allele description [Variation Report for NM_000390.4(CHM):c.1595C>A (p.Thr532Asn)]

NM_000390.4(CHM):c.1595C>A (p.Thr532Asn)

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.1595C>A (p.Thr532Asn)

HGVS:

NC_000023.11:g.85878979G>T
NG_009874.2:g.173584C>A
NM_000390.4:c.1595C>AMANE SELECT
NM_001320959.1:c.1151C>A
NM_001362517.1:c.1151C>A
NM_001362518.2:c.1151C>A
NM_001362519.1:c.1151C>A
NP_000381.1:p.Thr532Asn
NP_001307888.1:p.Thr384Asn
NP_001349446.1:p.Thr384Asn
NP_001349447.1:p.Thr384Asn
NP_001349448.1:p.Thr384Asn
LRG_699:g.173584C>A
NC_000023.10:g.85133984G>T

Protein change:

T384N

Links:

dbSNP: rs1924589059

NCBI 1000 Genomes Browser:

rs1924589059

Molecular consequence:

NM_000390.4:c.1595C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001320959.1:c.1151C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001362517.1:c.1151C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001362518.2:c.1151C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001362519.1:c.1151C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Rattus norvegicus olfactory receptor family 1 subfamily O member 2C (Or1o2c), mR...
Rattus norvegicus olfactory receptor family 1 subfamily O member 2C (Or1o2c), mRNA
gi|47576708|ref|NM_001001117.1|

Nucleotide
LOC126379708 [Pectinophora gossypiella]
LOC126379708 [Pectinophora gossypiella]
Gene ID:126379708

Gene
AGPAT2 [Gavialis gangeticus]
AGPAT2 [Gavialis gangeticus]
Gene ID:109292749

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001535663	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 17, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001535663

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 17, 2022)

germline

clinical testing

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001535663.4

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

Description

This variant has not been reported in the literature in individuals affected with CHM-related conditions. This sequence change replaces threonine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 532 of the CHM protein (p.Thr532Asn). This variant is not present in population databases (gnomAD no frequency). ClinVar contains an entry for this variant (Variation ID: 1038457). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CHM protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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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