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NM_018344.6(SLC29A3):c.59_60dup (p.Ser21fs) AND H syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 15, 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:
RCV003646023.1

Allele description [Variation Report for NM_018344.6(SLC29A3):c.59_60dup (p.Ser21fs)]

NM_018344.6(SLC29A3):c.59_60dup (p.Ser21fs)

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.59_60dup (p.Ser21fs)
HGVS:
  • NC_000010.11:g.71322811CA[3]
  • NG_017066.2:g.8553CA[3]
  • NM_001174098.2:c.59_60dup
  • NM_001363518.2:c.-178CA[3]
  • NM_018344.6:c.59_60dupMANE SELECT
  • NP_001167569.1:p.Ser21fs
  • NP_060814.4:p.Ser21fs
  • LRG_1318t1:c.59_60dup
  • LRG_1318:g.8553CA[3]
  • LRG_1318p1:p.Ser21fs
  • NC_000010.10:g.73082567_73082568insCA
  • NC_000010.10:g.73082568CA[3]
  • NR_033413.2:n.108CA[3]
  • NR_033414.2:n.108CA[3]
Protein change:
S21fs
Molecular consequence:
  • NM_001363518.2:c.-178CA[3] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001174098.2:c.59_60dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_018344.6:c.59_60dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_033413.2:n.108CA[3] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_033414.2:n.108CA[3] - 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
SCV004377423Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 15, 2023) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

SLC29A3 gene is mutated in pigmented hypertrichosis with insulin-dependent diabetes mellitus syndrome and interacts with the insulin signaling pathway.

Cliffe ST, Kramer JM, Hussain K, Robben JH, de Jong EK, de Brouwer AP, Nibbeling E, Kamsteeg EJ, Wong M, Prendiville J, James C, Padidela R, Becknell C, van Bokhoven H, Deen PM, Hennekam RC, Lindeman R, Schenck A, Roscioli T, Buckley MF.

Hum Mol Genet. 2009 Jun 15;18(12):2257-65. doi: 10.1093/hmg/ddp161. Epub 2009 Mar 31.

PubMed [citation]
PMID:
19336477

Human equilibrative nucleoside transporter-3 (hENT3) spectrum disorder mutations impair nucleoside transport, protein localization, and stability.

Kang N, Jun AH, Bhutia YD, Kannan N, Unadkat JD, Govindarajan R.

J Biol Chem. 2010 Sep 3;285(36):28343-52. doi: 10.1074/jbc.M110.109199. Epub 2010 Jul 1.

PubMed [citation]
PMID:
20595384
PMCID:
PMC2934698
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV004377423.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Ser21Glnfs*81) in the SLC29A3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC29A3 are known to be pathogenic (PMID: 19336477, 20595384, 23406517, 25963354). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SLC29A3-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Feb 28, 2024