NM_025000.4(DCAF17):c.95A>T (p.Asn32Ile) AND Woodhouse-Sakati syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 1, 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:: RCV002834358.9

Allele description [Variation Report for NM_025000.4(DCAF17):c.95A>T (p.Asn32Ile)]

NM_025000.4(DCAF17):c.95A>T (p.Asn32Ile)

Genes:

DCAF17:DDB1 and CUL4 associated factor 17 [Gene - OMIM - HGNC]
METTL8:methyltransferase 8, tRNA N3-cytidine [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q31.1

Genomic location:

Preferred name:

NM_025000.4(DCAF17):c.95A>T (p.Asn32Ile)

HGVS:

NC_000002.12:g.171434672A>T
NG_013038.2:g.5422A>T
NG_097077.1:g.280A>T
NG_097077.2:g.789A>T
NM_001164821.2:c.95A>T
NM_001321157.2:c.8+2T>A
NM_001321158.2:c.8+2T>A
NM_001321161.2:c.8+2T>A
NM_024770.5:c.-13+2T>A
NM_025000.4:c.95A>TMANE SELECT
NP_001158293.1:p.Asn32Ile
NP_079276.2:p.Asn32Ile
NC_000002.11:g.172291182A>T
NR_028482.2:n.447A>T

Protein change:

N32I

Molecular consequence:

NM_001164821.2:c.95A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_025000.4:c.95A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_028482.2:n.447A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001321157.2:c.8+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001321158.2:c.8+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001321161.2:c.8+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_024770.5:c.-13+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Woodhouse-Sakati syndrome
Synonyms:: Extrapyramidal disorder, progressive, with primary hypogonadism, mental retardation, and alopecia; Progressive extrapyramidal disorder with primary hypogonadism and alopecia; Woodhouse and Sakati syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009419; MedGen: C0342286; Orphanet: 3464; OMIM: 241080

Recent activity

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NADH dehydrogenase subunit 2 (mitochondrion) [Gomphocerippus rufus]
NADH dehydrogenase subunit 2 (mitochondrion) [Gomphocerippus rufus]
gi|301353421|ref|YP_003795645.1|

Protein
translation elongation factor 1-alpha, partial [Fusarium sporotrichioides]
translation elongation factor 1-alpha, partial [Fusarium sporotrichioides]
gi|2725935376|gb|XAJ24497.1|

Protein
LOC124900335 [Homo sapiens]
LOC124900335 [Homo sapiens]
Gene ID:124900335

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003214269	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 1, 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

SCV003214269

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 1, 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, SCV003214269.1

#	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 asparagine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 32 of the DCAF17 protein (p.Asn32Ile). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with DCAF17-related conditions. 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: Nov 10, 2024

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