NM_130468.4(CHST14):c.2T>C (p.Met1Thr) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Oct 2, 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:: RCV003443083.1

Allele description [Variation Report for NM_130468.4(CHST14):c.2T>C (p.Met1Thr)]

NM_130468.4(CHST14):c.2T>C (p.Met1Thr)

Genes:

LOC130056851:ATAC-STARR-seq lymphoblastoid silent region 6336 [Gene]
CHST14:carbohydrate sulfotransferase 14 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q15.1

Genomic location:

Preferred name:

NM_130468.4(CHST14):c.2T>C (p.Met1Thr)

HGVS:

NC_000015.10:g.40471215T>C
NG_017074.1:g.5255T>C
NM_130468.4:c.2T>CMANE SELECT
NP_569735.1:p.Met1Thr
NP_569735.1:p.Met1Thr
LRG_600t1:c.2T>C
LRG_600:g.5255T>C
LRG_600p1:p.Met1Thr
NC_000015.9:g.40763414T>C
NM_130468.3:c.2T>C

Protein change:

M1T

Molecular consequence:

NM_130468.4:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_130468.4:c.2T>C - 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
SCV004168445	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Oct 2, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004168445

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Oct 2, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV004168445.1

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

Description

Has not been previously published as pathogenic or benign to our knowledge; Not observed at significant frequency in large population cohorts (gnomAD); Initiation codon variant in a gene for which loss of function is a known mechanism of disease

#	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

Last Updated: Feb 28, 2024

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Relating variation to medicine