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NM_018344.6(SLC29A3):c.908AGA[1] (p.Lys304del) AND H syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 29, 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:
RCV002802175.3

Allele description [Variation Report for NM_018344.6(SLC29A3):c.908AGA[1] (p.Lys304del)]

NM_018344.6(SLC29A3):c.908AGA[1] (p.Lys304del)

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.908AGA[1] (p.Lys304del)
HGVS:
  • NC_000010.11:g.71362088AGA[1]
  • NG_017066.2:g.47830AGA[1]
  • NM_001174098.2:c.*137AGA[1]
  • NM_001363518.2:c.674AGA[1]
  • NM_018344.6:c.908AGA[1]MANE SELECT
  • NP_001350447.1:p.Lys226del
  • NP_060814.4:p.Lys304del
  • LRG_1318t1:c.908AGA[1]
  • LRG_1318:g.47830AGA[1]
  • LRG_1318p1:p.Lys304del
  • NC_000010.10:g.73121843_73121845del
  • NC_000010.10:g.73121845AGA[1]
  • NR_033413.2:n.876AGA[1]
  • NR_033414.2:n.649AGA[1]
Protein change:
K226del
Molecular consequence:
  • NM_001174098.2:c.*137AGA[1] - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001363518.2:c.674AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_018344.6:c.908AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NR_033413.2:n.876AGA[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_033414.2:n.649AGA[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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003209387Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 29, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV003209387.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant has not been reported in the literature in individuals affected with SLC29A3-related conditions. 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 is not present in population databases (gnomAD no frequency). This variant, c.911_913del, results in the deletion of 1 amino acid(s) of the SLC29A3 protein (p.Lys304del), but otherwise preserves the integrity of the reading frame.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024