VCV000262013.15 - ClinVar

NM_032122.5(DTNBP1):c.886C>T (p.Pro296Ser)

Germline

Classification

criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.

Benign/Likely benign

4 out of 6 submissions contributed to this 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.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_032122.5(DTNBP1):c.886C>T (p.Pro296Ser)

Variation ID: 262013 Accession: VCV000262013.15

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 6p22.3 6: 15523145 (GRCh38) [ NCBI UCSC ] 6: 15523376 (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 3, 2016	Jan 17, 2026	Feb 9, 2025

HGVS

Nucleotide	Protein	Molecular consequence
NM_032122.5:c.886C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_115498.2:p.Pro296Ser	missense
NM_001271667.2:c.643C>T	NP_001258596.1:p.Pro215Ser	missense
NM_001271668.2:c.835C>T	NP_001258597.1:p.Pro279Ser	missense
NM_001271669.2:c.781C>T	NP_001258598.1:p.Pro261Ser	missense
NC_000006.12:g.15523145G>A
NC_000006.11:g.15523376G>A
NG_009309.1:g.144896C>T
LRG_588:g.144896C>T
LRG_588t1:c.886C>T	LRG_588p1:p.Pro296Ser

... more HGVS ... less HGVS

Protein change

P296S, P215S, P279S, P261S

Other names

p.Pro296Ser

Canonical SPDI

NC_000006.12:15523144:G:A

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.

0.01198 (A)

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

The Genome Aggregation Database (gnomAD) 0.01341

1000 Genomes Project 30x 0.01343

Trans-Omics for Precision Medicine (TOPMed) 0.01505

1000 Genomes Project 0.01198

Exome Aggregation Consortium (ExAC) 0.00372

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01438

The Genome Aggregation Database (gnomAD), exomes 0.00316

The Genome Aggregation Database (gnomAD) 0.01236

Links

ClinGen: CA3643705 dbSNP: rs74907982 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.
DTNBP1		-	-	GRCh38 GRCh37	329	377

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.
not specified	Benign/Likely benign (2)	criteria provided, multiple submitters, no conflicts	Feb 9, 2025	RCV000248315.6
not provided	Benign/Likely benign (4)	criteria provided, multiple submitters, no conflicts	Jan 28, 2025	RCV000946920.13

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.	Expand all rows Collapse all rows 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.
Benign (-) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015)	NOT SPECIFIED	PreventionGenetics, part of Exact Sciences Accession: SCV000314888.1 First in ClinVar: Oct 03, 2016 Last updated: Oct 03, 2016	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Benign (Jan 28, 2025) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	not provided	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001093077.7 First in ClinVar: Dec 17, 2019 Last updated: Feb 25, 2025	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Likely benign (Feb 09, 2025) C Contributing to aggregate classification	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	not specified	Women's Health and Genetics/Laboratory Corporation of America, LabCorp Accession: SCV005886164.1 First in ClinVar: Mar 16, 2025 Last updated: Mar 16, 2025	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Likely benign (Oct 19, 2023) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015)	Not provided	Mayo Clinic Laboratories, Mayo Clinic Accession: SCV007324974.1 First in ClinVar: Jan 17, 2026 Last updated: Jan 17, 2026	Publications: PubMed (1) PubMed: 31898847 Comment: show BS1, BP4 (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown more Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Number of individuals with the variant: 12

Likely benign (-) N Not contributing to aggregate classification	no assertion criteria provided	not provided	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) Study: VKGL Data-share Consensus Accession: SCV001799134.1 First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: yes Observation 1 Collection method: clinical testing Allele origin: germline Affected status: yes

Likely benign (-) N Not contributing to aggregate classification	no assertion criteria provided	not provided	Genome Diagnostics Laboratory, University Medical Center Utrecht Additional submitter: Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV001931627.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: yes Observation 1 Collection method: clinical testing Allele origin: germline Affected status: yes

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Hermansky-Pudlak syndrome: Mutation update.	Huizing M	Human mutation	2020	PMID: 31898847

Text-mined citations for rs74907982 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jan 17, 2026

ClinVar Genomic variation as it relates to human health

NM_032122.5(DTNBP1):c.886C>T (p.Pro296Ser)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Citations for germline classification of this variant

Text-mined citations for rs74907982 ...