NM_000344.4(SMN1):c.346A>T (p.Ile116Phe) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 27, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002472926.5

Allele description [Variation Report for NM_000344.4(SMN1):c.346A>T (p.Ile116Phe)]

NM_000344.4(SMN1):c.346A>T (p.Ile116Phe)

Gene:

SMN1:survival of motor neuron 1, telomeric [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q13.2

Genomic location:

Preferred name:

NM_000344.4(SMN1):c.346A>T (p.Ile116Phe)

HGVS:

NC_000005.10:g.70942430A>T
NG_008691.1:g.22490A>T
NM_000344.4:c.346A>TMANE SELECT
NM_001297715.1:c.346A>T
NM_022874.2:c.346A>T
NP_000335.1:p.Ile116Phe
NP_001284644.1:p.Ile116Phe
NP_075012.1:p.Ile116Phe
LRG_676t1:c.346A>T
LRG_676:g.22490A>T
NC_000005.9:g.70238257A>T
NM_000344.3:c.346A>T
Q16637:p.Ile116Phe

Protein change:

I116F; ILE116PHE

Links:

UniProtKB: Q16637#VAR_034807; OMIM: 600354.0017; dbSNP: rs104893933

NCBI 1000 Genomes Browser:

rs104893933

Molecular consequence:

NM_000344.4:c.346A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001297715.1:c.346A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_022874.2:c.346A>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV002771655	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Jun 14, 2021)	unknown	clinical testing	PubMed (12) [See all records that cite these PMIDs] 15249625, 23136128, 28570645, 29982416, 19050931, 21329463, 31156382, 16301532, 17998247, 22101937, 21209906, 26467025
SCV004238364	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 27, 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

SCV002771655

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Pathogenic
(Jun 14, 2021)

unknown

clinical testing

PubMed (12)
[See all records that cite these PMIDs]

SCV004238364

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 27, 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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Detection of novel mutations in the SMN Tudor domain in type I SMA patients.

Cuscó I, Barceló MJ, del Río E, Baiget M, Tizzano EF.

Neurology. 2004 Jul 13;63(1):146-9.

PubMed [citation]

PMID:: 15249625

A novel function for the survival motoneuron protein as a translational regulator.

Sanchez G, Dury AY, Murray LM, Biondi O, Tadesse H, El Fatimy R, Kothary R, Charbonnier F, Khandjian EW, Côté J.

Hum Mol Genet. 2013 Feb 15;22(4):668-84. doi: 10.1093/hmg/dds474. Epub 2012 Nov 6.

PubMed [citation]

PMID:: 23136128

See all PubMed Citations (13)

Details of each submission

From Athena Diagnostics, SCV002771655.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (12)

Description

Frequency data for this variant in the general population cannot be distinguished from that of the SMN2 gene, and is therefore uninformative in assessment of variant pathogenicity (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)). Assessment of experimental evidence suggests this variant results in abnormal protein function. Studies indicate this variant leads to defective Sm core assembly (PMID: 16301532, 29982416). In multiple individuals, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic. The variant is located in a region that is considered important for protein function and/or structure.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV004238364.1

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

#	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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