NM_194255.4(SLC19A1):c.631TTC[1] (p.Phe212del) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 24, 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:: RCV002547809.10

Allele description [Variation Report for NM_194255.4(SLC19A1):c.631TTC[1] (p.Phe212del)]

NM_194255.4(SLC19A1):c.631TTC[1] (p.Phe212del)

Gene:

SLC19A1:solute carrier family 19 member 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

21q22.3

Genomic location:

Preferred name:

NM_194255.4(SLC19A1):c.631TTC[1] (p.Phe212del)

HGVS:

NC_000021.9:g.45531704AGA[1]
NG_028278.2:g.36437TTC[1]
NM_001205206.4:c.631TTC[1]
NM_001205207.3:c.511TTC[1]
NM_001352510.2:c.277TTC[1]
NM_001352511.3:c.631TTC[1]
NM_001352512.2:c.631TTC[1]
NM_194255.4:c.631TTC[1]MANE SELECT
NP_001192135.1:p.Phe212del
NP_001192136.1:p.Phe172del
NP_001339439.1:p.Phe94del
NP_001339440.1:p.Phe212del
NP_001339441.1:p.Phe212del
NP_919231.1:p.Phe212del
NC_000021.8:g.46951616_46951618del
NC_000021.8:g.46951618AGA[1]
NM_194255.3:c.634_636delTTC

Protein change:

F172del

Links:

OMIM: 600424.0001; dbSNP: rs757838708

NCBI 1000 Genomes Browser:

rs757838708

Molecular consequence:

NM_001205206.4:c.631TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001205207.3:c.511TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001352510.2:c.277TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001352511.3:c.631TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001352512.2:c.631TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_194255.4:c.631TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV003498256	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 24, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 32276275, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003498256

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 24, 2023)

germline

clinical testing

PubMed (2)
[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

A homozygous deletion in the SLC19A1 gene as a cause of folate-dependent recurrent megaloblastic anemia.

Svaton M, Skvarova Kramarzova K, Kanderova V, Mancikova A, Smisek P, Jesina P, Krijt J, Stiburkova B, Dobrovolny R, Sokolova J, Bakardjieva-Mihaylova V, Vodickova E, Rackova M, Stuchly J, Kalina T, Stary J, Trka J, Fronkova E, Kozich V.

Blood. 2020 Jun 25;135(26):2427-2431. doi: 10.1182/blood.2019003178. No abstract available.

PubMed [citation]

PMID:: 32276275
PMCID:: PMC7330012

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003498256.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant, c.634_636del, results in the deletion of 1 amino acid(s) of the SLC19A1 protein (p.Phe212del), but otherwise preserves the integrity of the reading frame. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has been observed in individual(s) with megaloblastic folate-dependent anaemia (PMID: 32276275). This variant is present in population databases (rs757838708, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant.

#	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: Nov 24, 2024

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