NM_013322.3(SNX10):c.151C>T (p.Arg51Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 22, 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:: RCV002550624.3

Allele description [Variation Report for NM_013322.3(SNX10):c.151C>T (p.Arg51Ter)]

NM_013322.3(SNX10):c.151C>T (p.Arg51Ter)

Gene:

SNX10:sorting nexin 10 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p15.2

Genomic location:

Preferred name:

NM_013322.3(SNX10):c.151C>T (p.Arg51Ter)

HGVS:

NC_000007.14:g.26364574C>T
NG_033902.1:g.77680C>T
NM_001199835.1:c.151C>T
NM_001199837.3:c.142C>T
NM_001199838.2:c.-41+72C>T
NM_001318198.1:c.229C>T
NM_001318199.3:c.151C>T
NM_001362753.1:c.229C>T
NM_001362754.1:c.229C>T
NM_013322.3:c.151C>TMANE SELECT
NP_001186764.1:p.Arg51Ter
NP_001186766.1:p.Arg48Ter
NP_001305127.1:p.Arg77Ter
NP_001305128.1:p.Arg51Ter
NP_001349682.1:p.Arg77Ter
NP_001349683.1:p.Arg77Ter
NP_037454.2:p.Arg51Ter
NC_000007.13:g.26404194C>T
NC_000007.13:g.26404194C>T

Protein change:

R48*

Links:

dbSNP: rs1353879401

NCBI 1000 Genomes Browser:

rs1353879401

Molecular consequence:

NM_001199838.2:c.-41+72C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001199835.1:c.151C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001199837.3:c.142C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001318198.1:c.229C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001318199.3:c.151C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001362753.1:c.229C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001362754.1:c.229C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_013322.3:c.151C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002963851	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 22, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 23123320, 23280965, 25811986, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002963851

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 22, 2022)

germline

clinical testing

PubMed (4)
[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

Homozygous stop mutation in the SNX10 gene in a consanguineous Iraqi boy with osteopetrosis and corpus callosum hypoplasia.

Mégarbané A, Pangrazio A, Villa A, Chouery E, Maarawi J, Sabbagh S, Lefranc G, Sobacchi C.

Eur J Med Genet. 2013 Jan;56(1):32-5. doi: 10.1016/j.ejmg.2012.10.010. Epub 2012 Oct 31.

PubMed [citation]

PMID:: 23123320

SNX10 mutations define a subgroup of human autosomal recessive osteopetrosis with variable clinical severity.

Pangrazio A, Fasth A, Sbardellati A, Orchard PJ, Kasow KA, Raza J, Albayrak C, Albayrak D, Vanakker OM, De Moerloose B, Vellodi A, Notarangelo LD, Schlack C, Strauss G, Kühl JS, Caldana E, Lo Iacono N, Susani L, Kornak U, Schulz A, Vezzoni P, Villa A, et al.

J Bone Miner Res. 2013 May;28(5):1041-9. doi: 10.1002/jbmr.1849.

PubMed [citation]

PMID:: 23280965

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002963851.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 804401). This variant has not been reported in the literature in individuals affected with SNX10-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Arg51*) in the SNX10 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SNX10 are known to be pathogenic (PMID: 23123320, 23280965, 25811986).

#	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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