VCV002501712.1 - ClinVar

NM_138386.3(NAF1):c.956_957del (p.Lys319fs)

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.

(1)

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.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_138386.3(NAF1):c.956_957del (p.Lys319fs)

Variation ID: 2501712 Accession: VCV002501712.1

Type and length

Deletion, 2 bp

Location

Cytogenetic: 4q32.2 4: 163133230-163133231 (GRCh38) [ NCBI UCSC ] 4: 164054382-164054383 (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	May 13, 2023	May 13, 2023	May 10, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_138386.3:c.956_957del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_612395.2:p.Lys319fs	frameshift
NM_001128931.2:c.956_957del	NP_001122403.1:p.Lys319fs	frameshift
NC_000004.12:g.163133233_163133234del
NC_000004.11:g.164054385_164054386del

Protein change

K319fs

Other names

Canonical SPDI

NC_000004.12:163133229:TTTTT:TTT

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

OMIM: 617868.0002 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.
NAF1		-	-	GRCh38 GRCh37	178	223

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.
Pulmonary fibrosis and/or bone marrow failure syndrome, telomere-related, 7	Pathogenic (1)	no assertion criteria provided	May 10, 2023	RCV003227583.1

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.
Pathogenic (May 10, 2023)	no assertion criteria provided Method: literature only	PULMONARY FIBROSIS AND/OR BONE MARROW FAILURE SYNDROME, TELOMERE-RELATED, 7 Affected status: not provided Allele origin: germline	OMIM Accession: SCV003924092.1 First in ClinVar: May 13, 2023 Last updated: May 13, 2023	Publications: PubMed (1) PubMed: 27510903 Comment on evidence: In a 57-year-old woman (JH2) with telomere-related pulmonary fibrosis and/or bone marrow failure syndrome-7 (PFBMFT7; 620365), Stanley et al. (2016) identified a heterozygous 2-bp deletion … (more) In a 57-year-old woman (JH2) with telomere-related pulmonary fibrosis and/or bone marrow failure syndrome-7 (PFBMFT7; 620365), Stanley et al. (2016) identified a heterozygous 2-bp deletion (c.956_957delAA) in exon 7 of the NAF1 gene, resulting in a frameshift and premature termination (Lys319ArgfsTer21). The mutation, which was found by whole-genome sequencing, segregated with the disorder in the family. It was not present in 9,006 individuals in public databases or in 134 in-house controls. She had no family history of the disorder, and the deceased parents were not sequenced. Expression of the mutation into HeLa cells showed presence of a truncated protein that did not reduce TERC (602322) levels, indicating that it did not cause a dominant-negative effect. However, K319fs was unable to rescue low TERC levels in NAF1-null HeLa cells, consistent with a loss of function. The mutation disrupted the nuclear localization signal, and the truncated protein localized to the cytoplasm. (less)

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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Loss-of-function mutations in the RNA biogenesis factor NAF1 predispose to pulmonary fibrosis-emphysema.	Stanley SE	Science translational medicine	2016	PMID: 27510903

Text-mined citations for this variant ...

Record last updated Dec 02, 2023

ClinVar Genomic variation as it relates to human health

NM_138386.3(NAF1):c.956_957del (p.Lys319fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...