NM_001174147.2(LMX1B):c.958G>A (p.Val320Met) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 15, 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:: RCV001338895.7

Allele description [Variation Report for NM_001174147.2(LMX1B):c.958G>A (p.Val320Met)]

NM_001174147.2(LMX1B):c.958G>A (p.Val320Met)

Gene:

LMX1B:LIM homeobox transcription factor 1 beta [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q33.3

Genomic location:

Preferred name:

NM_001174147.2(LMX1B):c.958G>A (p.Val320Met)

HGVS:

NC_000009.12:g.126695910G>A
NG_017039.1:g.86468G>A
NM_001174146.2:c.991G>A
NM_001174147.2:c.958G>AMANE SELECT
NM_002316.4:c.958G>A
NP_001167617.1:p.Val331Met
NP_001167618.1:p.Val320Met
NP_002307.2:p.Val320Met
LRG_1014t1:c.958G>A
LRG_1014t2:c.991G>A
LRG_1014t3:c.958G>A
LRG_1014:g.86468G>A
LRG_1014p1:p.Val320Met
LRG_1014p2:p.Val331Met
LRG_1014p3:p.Val320Met
NC_000009.11:g.129458189G>A

Protein change:

V320M

Links:

dbSNP: rs778847250

NCBI 1000 Genomes Browser:

rs778847250

Molecular consequence:

NM_001174146.2:c.991G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001174147.2:c.958G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002316.4:c.958G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

MULTISPECIES: DUF441 domain-containing protein [Bacillus]
MULTISPECIES: DUF441 domain-containing protein [Bacillus]
gi|490533523|ref|WP_004398695.1|

Protein
Homo sapiens receptor interacting serine/threonine kinase 2 (RIPK2), transcript ...
Homo sapiens receptor interacting serine/threonine kinase 2 (RIPK2), transcript variant 1, mRNA
gi|1519311484|ref|NM_003821.6|

Nucleotide
Escherichia coli str. K-12 substr. MG1655, complete genome
Escherichia coli str. K-12 substr. MG1655, complete genome
gi|1929623242|gb|CP032679.1|

Nucleotide
MAG: U32 family peptidase [Sedimenticola sp.]
MAG: U32 family peptidase [Sedimenticola sp.]
gi|1321811068|gb|PLY16568.1||gnl|WG O|C0631_03615

Protein
MAG: aspartate aminotransferase family protein [Candidatus Nitrosopelagicus sp.]
MAG: aspartate aminotransferase family protein [Candidatus Nitrosopelagicus sp.]
gi|2033930127|dbj|GIT55145.1||gnl|W EA|GIT55145

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001532600	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 15, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001532600

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 15, 2024)

germline

clinical testing

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

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001532600.4

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

Description

This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 320 of the LMX1B protein (p.Val320Met). This variant is present in population databases (rs778847250, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with LMX1B-related conditions. ClinVar contains an entry for this variant (Variation ID: 1035953). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt LMX1B protein function with a negative predictive value of 80%. 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.

#	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: Sep 29, 2024

ClinVar

Relating variation to medicine