NM_018344.6(SLC29A3):c.946TTC[1] (p.Phe317del) AND H syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 24, 2023
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:: RCV003645967.2

Allele description [Variation Report for NM_018344.6(SLC29A3):c.946TTC[1] (p.Phe317del)]

NM_018344.6(SLC29A3):c.946TTC[1] (p.Phe317del)

Gene:

SLC29A3:solute carrier family 29 member 3 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

10q22.1

Genomic location:

Preferred name:

NM_018344.6(SLC29A3):c.946TTC[1] (p.Phe317del)

HGVS:

NC_000010.11:g.71362126TTC[1]
NG_017066.2:g.47868TTC[1]
NM_001174098.2:c.*175TTC[1]
NM_001363518.2:c.712TTC[1]
NM_018344.6:c.946TTC[1]MANE SELECT
NP_001350447.1:p.Phe239del
NP_060814.4:p.Phe317del
LRG_1318t1:c.946TTC[1]
LRG_1318:g.47868TTC[1]
LRG_1318p1:p.Phe317del
NC_000010.10:g.73121881_73121883del
NC_000010.10:g.73121883TTC[1]
NR_033413.2:n.914TTC[1]
NR_033414.2:n.687TTC[1]

Protein change:

F239del

Molecular consequence:

NM_001174098.2:c.*175TTC[1] - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001363518.2:c.712TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_018344.6:c.946TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_033413.2:n.914TTC[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_033414.2:n.687TTC[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: H syndrome
Synonyms:: Histiocytosis with joint contractures and sensorineural deafness; Faisalabad histiocytosis; HISTIOCYTOSIS AND LYMPHADENOPATHY WITH OR WITHOUT CUTANEOUS, CARDIAC, AND/OR ENDOCRINE FEATURES, JOINT CONTRACTURES, AND/OR DEAFNESS; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011273; MedGen: C1864445; Orphanet: 168569; OMIM: 602782

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Homo sapiens mitochondrial ribosomal protein S17, mRNA (cDNA clone MGC:64897 IMA...
Homo sapiens mitochondrial ribosomal protein S17, mRNA (cDNA clone MGC:64897 IMAGE:6173349), complete cds
gi|34784672|gb|BC054031.2|

Nucleotide
yaiE [Escherichia coli O157:H7 str. Sakai]
yaiE [Escherichia coli O157:H7 str. Sakai]
Gene ID:914543

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004370680	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 24, 2023)	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

SCV004370680

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 24, 2023)

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, SCV004370680.1

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

Description

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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with SLC29A3-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.949_951del, results in the deletion of 1 amino acid(s) of the SLC29A3 protein (p.Phe317del), but otherwise preserves the integrity of the reading frame.

#	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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