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NM_001371623.1(TCOF1):c.1390G>A (p.Ala464Thr) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jun 24, 2022
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:
RCV004029890.1

Allele description [Variation Report for NM_001371623.1(TCOF1):c.1390G>A (p.Ala464Thr)]

NM_001371623.1(TCOF1):c.1390G>A (p.Ala464Thr)

Gene:
TCOF1:treacle ribosome biogenesis factor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q32
Genomic location:
Preferred name:
NM_001371623.1(TCOF1):c.1390G>A (p.Ala464Thr)
HGVS:
  • NC_000005.10:g.150375065G>A
  • NG_011341.1:g.22427G>A
  • NM_000356.4:c.1159G>A
  • NM_001008657.3:c.1390G>A
  • NM_001135243.2:c.1390G>A
  • NM_001135244.2:c.1390G>A
  • NM_001135245.2:c.1159G>A
  • NM_001195141.2:c.1390G>A
  • NM_001371623.1:c.1390G>AMANE SELECT
  • NP_000347.2:p.Ala387Thr
  • NP_001008657.1:p.Ala464Thr
  • NP_001128715.1:p.Ala464Thr
  • NP_001128715.1:p.Ala464Thr
  • NP_001128716.1:p.Ala464Thr
  • NP_001128717.1:p.Ala387Thr
  • NP_001182070.1:p.Ala464Thr
  • NP_001358552.1:p.Ala464Thr
  • NC_000005.9:g.149754628G>A
  • NC_000005.9:g.149754628G>A
  • NM_001135243.1:c.1390G>A
Protein change:
A387T
Links:
dbSNP: rs150956690
NCBI 1000 Genomes Browser:
rs150956690
Molecular consequence:
  • NM_000356.4:c.1159G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001008657.3:c.1390G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001135243.2:c.1390G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001135244.2:c.1390G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001135245.2:c.1159G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195141.2:c.1390G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371623.1:c.1390G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004963639Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Jun 24, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV004963639.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 13, 2024