NM_018344.6(SLC29A3):c.479G>A (p.Trp160Ter) AND H syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 28, 2017
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:: RCV000695799.5

Allele description [Variation Report for NM_018344.6(SLC29A3):c.479G>A (p.Trp160Ter)]

NM_018344.6(SLC29A3):c.479G>A (p.Trp160Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

10q22.1

Genomic location:

Preferred name:

NM_018344.6(SLC29A3):c.479G>A (p.Trp160Ter)

HGVS:

NC_000010.11:g.71351657G>A
NG_017066.2:g.37399G>A
NM_001174098.2:c.479G>A
NM_001363518.2:c.245G>A
NM_018344.6:c.479G>AMANE SELECT
NP_001167569.1:p.Trp160Ter
NP_001350447.1:p.Trp82Ter
NP_060814.4:p.Trp160Ter
LRG_1318t1:c.479G>A
LRG_1318:g.37399G>A
LRG_1318p1:p.Trp160Ter
NC_000010.10:g.73111414G>A
NM_018344.5:c.479G>A
NR_033413.2:n.447G>A

Protein change:

W160*

Links:

dbSNP: rs776960135

NCBI 1000 Genomes Browser:

rs776960135

Molecular consequence:

NR_033413.2:n.447G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001174098.2:c.479G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001363518.2:c.245G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_018344.6:c.479G>A - nonsense - [Sequence Ontology: SO:0001587]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000824320	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 28, 2017)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 19336477, 20595384, 23406517, 25963354, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000824320

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 28, 2017)

germline

clinical testing

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

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

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, SCV000824320.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in SLC29A3 are known to be pathogenic (PMID: 19336477, 20595384, 23406517, 25963354). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with SLC29A3-related disease. This variant is present in population databases (rs776960135, ExAC 0.009%). This sequence change creates a premature translational stop signal (p.Trp160*) in the SLC29A3 gene. It is expected to result in an absent or disrupted protein product.

#	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: Apr 15, 2024

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