NM_024665.7(TBL1XR1):c.935T>C (p.Leu312Ser) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 18, 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:: RCV004474170.1

Allele description [Variation Report for NM_024665.7(TBL1XR1):c.935T>C (p.Leu312Ser)]

NM_024665.7(TBL1XR1):c.935T>C (p.Leu312Ser)

Genes:

LOC126806878:CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:176755168-176756367 [Gene]
TBL1XR1:TBL1X/Y related 1 [Gene - OMIM - HGNC]
TBL1XR1-AS1:TBL1XR1 antisense RNA 1 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q26.32

Genomic location:

Preferred name:

NM_024665.7(TBL1XR1):c.935T>C (p.Leu312Ser)

HGVS:

NC_000003.12:g.177038425A>G
NG_047195.1:g.163836T>C
NG_083198.1:g.1146A>G
NM_001321193.3:c.935T>C
NM_001321194.3:c.935T>C
NM_001321195.3:c.674T>C
NM_001374327.1:c.935T>C
NM_001374328.1:c.935T>C
NM_001374329.1:c.935T>C
NM_001374330.1:c.674T>C
NM_024665.7:c.935T>CMANE SELECT
NP_001308122.1:p.Leu312Ser
NP_001308123.1:p.Leu312Ser
NP_001308124.1:p.Leu225Ser
NP_001361256.1:p.Leu312Ser
NP_001361257.1:p.Leu312Ser
NP_001361258.1:p.Leu312Ser
NP_001361259.1:p.Leu225Ser
NP_078941.2:p.Leu312Ser
NC_000003.11:g.176756213A>G
NM_024665.4:c.935T>C
NR_174966.1:n.404A>G

Protein change:

L225S

Molecular consequence:

NM_001321193.3:c.935T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001321194.3:c.935T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001321195.3:c.674T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374327.1:c.935T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374328.1:c.935T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374329.1:c.935T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374330.1:c.674T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_024665.7:c.935T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_174966.1:n.404A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

Recent activity

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anthranilate synthase beta subunit 1 [Arabidopsis thaliana]
anthranilate synthase beta subunit 1 [Arabidopsis thaliana]
gi|15222532|ref|NP_173893.1|

Protein
Peperomia tutuilana (1962)
Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004962139	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jan 18, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004962139

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jan 18, 2024)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV004962139.1

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

Description

The c.935T>C (p.L312S) alteration is located in exon 11 (coding exon 9) of the TBL1XR1 gene. This alteration results from a T to C substitution at nucleotide position 935, causing the leucine (L) at amino acid position 312 to be replaced by a serine (S). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. This missense alteration is located in a region that has a low rate of benign missense variation (Lek, 2016; Firth, 2009). This alteration is predicted to be deleterious by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

#	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: May 7, 2024

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