NM_018389.5(SLC35C1):c.503_505del (p.Phe168del) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:: Jun 8, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000513734.30

Allele description [Variation Report for NM_018389.5(SLC35C1):c.503_505del (p.Phe168del)]

NM_018389.5(SLC35C1):c.503_505del (p.Phe168del)

Gene:

SLC35C1:solute carrier family 35 member C1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11p11.2

Genomic location:

Preferred name:

NM_018389.5(SLC35C1):c.503_505del (p.Phe168del)

HGVS:

NC_000011.10:g.45806304_45806306del
NG_009875.1:g.7233_7235del
NM_001145265.2:c.464_466del
NM_001145266.2:c.464_466delTCT
NM_018389.5:c.503_505delMANE SELECT
NM_018389.5:c.503_505delTCT
NP_001138737.1:p.Phe155del
NP_001138738.1:p.Phe155del
NP_001138738.1:p.Phe155del
NP_060859.4:p.Phe168del
NP_060859.4:p.Phe168del
NP_060859.4:p.Phe168del
LRG_107t1:c.503_505del
LRG_107:g.7233_7235del
LRG_107p1:p.Phe168del
NC_000011.9:g.45827853_45827855del
NC_000011.9:g.45827855_45827857del
NM_001145265.1:c.464_466delTCT
NM_001145266.1:c.464_466del
NM_018389.4:c.503_505del
NM_018389.4:c.503_505delTCT
NM_018389.5:c.503_505del
NM_018389.5:c.503_505delTCTMANE SELECT

Protein change:

F155del

Links:

OMIM: 605881.0004; dbSNP: rs587777655

NCBI 1000 Genomes Browser:

rs587777655

Molecular consequence:

NM_001145265.2:c.464_466del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_018389.5:c.503_505del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001145266.2:c.464_466delTCT - inframe_indel - [Sequence Ontology: SO:0001820]

Observations:

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
SCV000331279	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Sep 23, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV000609671	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 30, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000709992	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Jun 8, 2023)	germline	clinical testing	Citation Link,
SCV001248264	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely pathogenic (Nov 1, 2020)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	3	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Molecular diagnostic testing for congenital disorders of glycosylation (CDG): detection rate for single gene testing and next generation sequencing panel testing.

Jones MA, Rhodenizer D, da Silva C, Huff IJ, Keong L, Bean LJ, Coffee B, Collins C, Tanner AK, He M, Hegde MR.

Mol Genet Metab. 2013 Sep-Oct;110(1-2):78-85. doi: 10.1016/j.ymgme.2013.05.012. Epub 2013 May 28.

PubMed [citation]

PMID:: 23806237

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Eurofins Ntd Llc (ga), SCV000331279.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	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		3	not provided	not provided	not provided

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000609671.1

#	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	not provided	not provided	not provided	not provided		not provided	0.000486	not provided	not provided

From GeneDx, SCV000709992.5

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

Description

In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 23891399, 32313197, 34389986, 35338746, 23806237, 24403049, 33144682, 29030401)

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

From CeGaT Center for Human Genetics Tuebingen, SCV001248264.20

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

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

Last Updated: Apr 15, 2024

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