NM_005869.4(CWC27):c.100C>A (p.Pro34Thr) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 21, 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:: RCV001368561.7

Allele description

NM_005869.4(CWC27):c.100C>A (p.Pro34Thr)

Gene:

CWC27:CWC27 spliceosome associated cyclophilin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q12.3

Genomic location:

Preferred name:

NM_005869.4(CWC27):c.100C>A (p.Pro34Thr)

HGVS:

NC_000005.10:g.64774748C>A
NM_001297644.1:c.100C>A
NM_001297645.2:c.100C>A
NM_001318000.2:c.100C>A
NM_001364478.1:c.100C>A
NM_005869.4:c.100C>AMANE SELECT
NP_001284573.1:p.Pro34Thr
NP_001284574.1:p.Pro34Thr
NP_001304929.1:p.Pro34Thr
NP_001351407.1:p.Pro34Thr
NP_005860.2:p.Pro34Thr
NC_000005.9:g.64070575C>A

Protein change:

P34T

Links:

dbSNP: rs141974787

NCBI 1000 Genomes Browser:

rs141974787

Molecular consequence:

NM_001297644.1:c.100C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001297645.2:c.100C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318000.2:c.100C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001364478.1:c.100C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_005869.4:c.100C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens ankyrin repeat and SOCS box containing 5 (ASB5), transcript variant...
Homo sapiens ankyrin repeat and SOCS box containing 5 (ASB5), transcript variant 2, mRNA
gi|2287478760|ref|NM_001410863.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001564959	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 21, 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

SCV001564959

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 21, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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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 Invitae, SCV001564959.4

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

Description

This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 34 of the CWC27 protein (p.Pro34Thr). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with CWC27-related conditions. ClinVar contains an entry for this variant (Variation ID: 1059307). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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: Dec 24, 2023

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