NM_000154.2(GALK1):c.857G>A (p.Arg286Gln) AND Deficiency of galactokinase

Germline classification:: Benign (2 submissions)
Last evaluated:: Jan 22, 2024
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:: RCV000952402.9

Allele description [Variation Report for NM_000154.2(GALK1):c.857G>A (p.Arg286Gln)]

NM_000154.2(GALK1):c.857G>A (p.Arg286Gln)

Gene:

GALK1:galactokinase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q25.1

Genomic location:

Preferred name:

NM_000154.2(GALK1):c.857G>A (p.Arg286Gln)

HGVS:

NC_000017.11:g.75758536C>T
NG_007372.1:g.42102C>T
NG_008079.1:g.11664G>A
NM_000154.2:c.857G>AMANE SELECT
NP_000145.1:p.Arg286Gln
LRG_1430t1:c.857G>A
LRG_1430p1:p.Arg286Gln
NC_000017.10:g.73754617C>T
NM_000154.1:c.857G>A

Protein change:

R286Q

Links:

dbSNP: rs145641205

NCBI 1000 Genomes Browser:

rs145641205

Molecular consequence:

NM_000154.2:c.857G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Deficiency of galactokinase
Synonyms:: GALACTOSEMIA II; Galactosemia 2; Hereditary galactokinase deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009255; MedGen: C0268155; Orphanet: 352; OMIM: 230200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001098902	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 22, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001459337	Natera, Inc.	no assertion criteria provided	Likely benign (Jun 18, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001098902

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 22, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001459337

Natera, Inc.

no assertion criteria provided

Likely benign
(Jun 18, 2020)

germline

clinical testing

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

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001098902.6

#	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

From Natera, Inc., SCV001459337.1

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

Last Updated: Mar 16, 2024

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