VCV002599057.4 - ClinVar

NM_005573.4(LMNB1):c.1361T>C (p.Ile454Thr)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(3)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_005573.4(LMNB1):c.1361T>C (p.Ile454Thr)

Variation ID: 2599057 Accession: VCV002599057.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 5q23.2 5: 126821110 (GRCh38) [ NCBI UCSC ] 5: 126156802 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Oct 28, 2023	Nov 17, 2024	Oct 26, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_005573.4:c.1361T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_005564.1:p.Ile454Thr	missense
NM_001198557.2:c.731T>C	NP_001185486.1:p.Ile244Thr	missense
NR_134488.1:n.2325T>C		non-coding transcript variant
NR_177109.1:n.4099T>C		non-coding transcript variant
NC_000005.10:g.126821110T>C
NC_000005.9:g.126156802T>C
NG_008360.2:g.48970T>C

... more HGVS ... less HGVS

Protein change

I454T, I244T

Other names

Canonical SPDI

NC_000005.10:126821109:T:C

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
LMNB1		No evidence available	Sufficient evidence for dosage pathogenicity	GRCh38 GRCh37	247	286

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
LMNB1-related disorder	Uncertain significance (1)	criteria provided, single submitter	Mar 31, 2023	RCV003434754.4
Inborn genetic diseases	Uncertain significance (1)	criteria provided, single submitter	Aug 10, 2023	RCV003356493.2
Microcephaly 26, primary, autosomal dominant	Uncertain significance (1)	criteria provided, single submitter	Oct 26, 2023	RCV004784145.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Mar 31, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	LMNB1-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004117342.1 First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023	Comment: The LMNB1 c.1361T>C variant is predicted to result in the amino acid substitution p.Ile454Thr. To our knowledge, this variant has not been reported in the … (more) The LMNB1 c.1361T>C variant is predicted to result in the amino acid substitution p.Ile454Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0035% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/5-126156802-T-C). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. (less)
Uncertain significance (Aug 10, 2023)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Inborn genetic diseases Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV004062980.2 First in ClinVar: Oct 28, 2023 Last updated: May 01, 2024	Comment: The c.1361T>C (p.I454T) alteration is located in exon 7 (coding exon 7) of the LMNB1 gene. This alteration results from a T to C substitution … (more) The c.1361T>C (p.I454T) alteration is located in exon 7 (coding exon 7) of the LMNB1 gene. This alteration results from a T to C substitution at nucleotide position 1361, causing the isoleucine (I) at amino acid position 454 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)
Uncertain significance (Oct 26, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Microcephaly 26, primary, autosomal dominant (Autosomal dominant inheritance) Affected status: yes Allele origin: germline	Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center Accession: SCV005397645.1 First in ClinVar: Nov 17, 2024 Last updated: Nov 17, 2024	Comment: This sequence variant is a single nucleotide substitution (T>C) at position 1361 of the coding sequence of the LMNB1 gene that results in an isoleucine … (more) This sequence variant is a single nucleotide substitution (T>C) at position 1361 of the coding sequence of the LMNB1 gene that results in an isoleucine to threonine amino acid change at residue 454 of the lamin B1 protein. This variant is absent from ClinVar but is present in 7 of 402692 alleles (0.0017%) in the gnomAD population dataset. To our knowledge, this variant has not been observed in an individual with a LMNB1-related disorder in the published literature. Multiple bioinformatic tools predict that this isoleucine to threonine amino acid change would be damaging, and the Ile454 residue at this position is highly conserved across the vertebrate species examined. Studies examining the functional consequence of this variant have not been published, to our knowledge. At this time, there is insufficient evidence to determine if this variant is pathogenic or benign. Therefore, we consider this a variant of uncertain significance. ACMG Criteria: PM2, PP2, PP3 (less)

Comment:

The LMNB1 c.1361T>C variant is predicted to result in the amino acid substitution p.Ile454Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0035% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/5-126156802-T-C). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

Comment:

The c.1361T>C (p.I454T) alteration is located in exon 7 (coding exon 7) of the LMNB1 gene. This alteration results from a T to C substitution at nucleotide position 1361, causing the isoleucine (I) at amino acid position 454 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

Comment:

This sequence variant is a single nucleotide substitution (T>C) at position 1361 of the coding sequence of the LMNB1 gene that results in an isoleucine to threonine amino acid change at residue 454 of the lamin B1 protein. This variant is absent from ClinVar but is present in 7 of 402692 alleles (0.0017%) in the gnomAD population dataset. To our knowledge, this variant has not been observed in an individual with a LMNB1-related disorder in the published literature. Multiple bioinformatic tools predict that this isoleucine to threonine amino acid change would be damaging, and the Ile454 residue at this position is highly conserved across the vertebrate species examined. Studies examining the functional consequence of this variant have not been published, to our knowledge. At this time, there is insufficient evidence to determine if this variant is pathogenic or benign. Therefore, we consider this a variant of uncertain significance. ACMG Criteria: PM2, PP2, PP3

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Nov 19, 2024

ClinVar Genomic variation as it relates to human health

NM_005573.4(LMNB1):c.1361T>C (p.Ile454Thr)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...