VCV002626860.2 - ClinVar

NM_001145304.2(IQCN):c.910C>T (p.Gln304Ter)

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.

(2)

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.

Likely pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001145304.2(IQCN):c.910C>T (p.Gln304Ter)

Variation ID: 2626860 Accession: VCV002626860.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 19p13.11 19: 18266630 (GRCh38) [ NCBI UCSC ] 19: 18377440 (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	Mar 23, 2024	Mar 3, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001145304.2:c.910C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001138776.1:p.Gln304Ter	nonsense
NM_001145305.2:c.772C>T	NP_001138777.1:p.Gln258Ter	nonsense
NM_025249.4:c.910C>T	NP_079525.1:p.Gln304Ter	nonsense
NC_000019.10:g.18266630G>A
NC_000019.9:g.18377440G>A

... more HGVS ... less HGVS

Protein change

Q304*, Q258*

Other names

Canonical SPDI

NC_000019.10:18266629:G:A

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: 620160.0001 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.
IQCN		-	-	GRCh38 GRCh37	147	158

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.
Spermatogenic failure 78	Likely pathogenic (2)	criteria provided, single submitter	Mar 3, 2024	RCV003387497.2

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.
Likely pathogenic (Mar 03, 2024)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: curation	Spermatogenic failure 78 Affected status: yes Allele origin: unknown	SIB Swiss Institute of Bioinformatics Accession: SCV004801356.1 First in ClinVar: Mar 23, 2024 Last updated: Mar 23, 2024	Publications: PubMed (1) PubMed: 36321563 Comment: This variant is interpreted for Spermatogenic failure 78, autosomal recessive. The following ACMG Tag(s) were applied: Absent from controls (or at extremely low frequency if … (more) This variant is interpreted for Spermatogenic failure 78, autosomal recessive. The following ACMG Tag(s) were applied: Absent from controls (or at extremely low frequency if recessive) in gnomAD (PM2). Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants (PM4). Well-established functional studies show a deleterious effect (PS3-moderate). (less)
Pathogenic (Dec 16, 2022)	no assertion criteria provided Method: literature only	SPERMATOGENIC FAILURE 78 Affected status: not provided Allele origin: germline	OMIM Accession: SCV004098988.1 First in ClinVar: Oct 28, 2023 Last updated: Oct 28, 2023	Publications: PubMed (1) PubMed: 36321563 Comment on evidence: In an infertile Han Chinese man (family 1) with spermatogenic failure due to a manchette assembly defect of the acrosome (SPGF78; 620170), Dai et al. … (more) In an infertile Han Chinese man (family 1) with spermatogenic failure due to a manchette assembly defect of the acrosome (SPGF78; 620170), Dai et al. (2022) identified homozygosity for a c.910C-T transition (c.910C-T, NM_001145304.2) in exon 3 of the IQCN gene, resulting in a gln304-to-ter (Q304X) substitution causing loss of 5 IQ motifs. His unaffected parents were heterozygous for the mutation, which was not found in 100 men with normal fertility or in the East Asian populations of the ExAC or gnomAD databases. (less)

Comment:

This variant is interpreted for Spermatogenic failure 78, autosomal recessive. The following ACMG Tag(s) were applied: Absent from controls (or at extremely low frequency if recessive) in gnomAD (PM2). Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants (PM4). Well-established functional studies show a deleterious effect (PS3-moderate).

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

Title	Author	Journal	Year	Link
IQCN disruption causes fertilization failure and male infertility due to manchette assembly defect.	Dai J	EMBO molecular medicine	2022	PMID: 36321563

Text-mined citations for this variant ...

Record last updated Mar 23, 2024

ClinVar Genomic variation as it relates to human health

NM_001145304.2(IQCN):c.910C>T (p.Gln304Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...