ClinVar Genomic variation as it relates to human health
NM_024824.5(ZC3H14):c.2204+17_2204+41del
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.
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_024824.5(ZC3H14):c.2204+17_2204+41del
Variation ID: 254279 Accession: VCV000254279.17
- Type and length
-
Deletion, 25 bp
- Location
-
Cytogenetic: 14q31.3 14: 88610948-88610972 (GRCh38) [ NCBI UCSC ] 14: 89077292-89077316 (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 Sep 25, 2016 Apr 15, 2024 Jan 1, 2024 - HGVS
- ... more HGVS ... less HGVS
- Protein change
- Other names
- -
- Canonical SPDI
- NC_000014.9:88610947:TTCAAATTCGTTTTTCTCATGTCAGTTCAAATTC:TTCAAATTC
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
-
-
Global minor allele
frequency (GMAF) HelpThe 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.
-
0.00599 (TTCAAATTC)
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
- Comment on variant
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 | ||
---|---|---|---|---|---|---|
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. |
|||
ZC3H14 | - | - |
GRCh38 GRCh37 |
86 | 142 |
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. |
---|---|---|---|---|
Conflicting interpretations of pathogenicity (2) |
no assertion criteria provided
|
Dec 2, 2021 | RCV000240871.6 | |
Benign (3) |
criteria provided, multiple submitters, no conflicts
|
Jan 1, 2024 | RCV000966173.12 |
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. |
|
---|---|---|---|---|---|
Benign
(Dec 31, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Invitae
Accession: SCV001113465.2
First in ClinVar: Dec 17, 2019 Last updated: May 04, 2020 |
|
|
Benign
(May 20, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Knight Diagnostic Laboratories, Oregon Health and Sciences University
Accession: SCV001449013.1
First in ClinVar: Dec 11, 2020 Last updated: Dec 11, 2020 |
Number of individuals with the variant: 1
Clinical Features:
Spastic paraplegia (present) , Intellectual disability (present) , Glaucoma (present)
Sex: female
|
|
Benign
(Jan 01, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV003917339.7
First in ClinVar: Apr 23, 2023 Last updated: Apr 15, 2024 |
Comment:
ZC3H14: BS1, BS2
Number of individuals with the variant: 15
|
|
Benign
(Jan 06, 2020)
|
no assertion criteria provided
Method: curation
|
Mental retardation, autosomal recessive 56
Affected status: unknown
Allele origin:
germline
|
Reproductive Health Research and Development, BGI Genomics
Accession: SCV001142443.1
First in ClinVar: Jan 12, 2020 Last updated: Jan 12, 2020 |
Comment:
NG_050601.1(NM_024824.4):c.2204+17_2204+41del in ZC3H14 gene has an allele frequency of 0.028 in Ashkenazi Jewish subpopulation in the gnomAD database, including 22 homozygous occurrences. Benign computational verdict … (more)
NG_050601.1(NM_024824.4):c.2204+17_2204+41del in ZC3H14 gene has an allele frequency of 0.028 in Ashkenazi Jewish subpopulation in the gnomAD database, including 22 homozygous occurrences. Benign computational verdict because benign prediction from GERP. Pak et al. reported three intellectual disability patients in a consanguineous family with the homozygous of this deletion. Haplotype of the single linkage interval with maximum LOD score of 2.5 in Family-2 (PMID: 21734151). Taken together, we interprete this variant as Benign/Likely benign variant. ACMG/AMP criteria applied: BS1, BS2, BP4, PM3_Supporting, PP1_Strong. (less)
|
|
Pathogenic
(Dec 02, 2021)
|
no assertion criteria provided
Method: literature only
|
INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 56
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000299369.2
First in ClinVar: Sep 25, 2016 Last updated: Dec 12, 2021 |
Comment on evidence:
In 3 brothers, born of consanguineous Iranian parents (family M168), with autosomal recessive intellectual developmental disorder-56 (MRT56; 617125), Pak et al. (2011) identified a homozygous … (more)
In 3 brothers, born of consanguineous Iranian parents (family M168), with autosomal recessive intellectual developmental disorder-56 (MRT56; 617125), Pak et al. (2011) identified a homozygous 25-bp deletion in the ZC3H14 gene located 16 bp downstream of exon 16, which is common to all 4 isoforms. The deletion segregated with the disorder in the family and was not found to be homozygous in 831 control individuals. Functional studies of the variant and studies of patient cells were not performed. (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
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
Mutation of the conserved polyadenosine RNA binding protein, ZC3H14/dNab2, impairs neural function in Drosophila and humans. | Pak C | Proceedings of the National Academy of Sciences of the United States of America | 2011 | PMID: 21734151 |
Text-mined citations for rs571303442 ...
HelpRecord last updated Apr 15, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.
NCBI staff reviewed the sequence information reported in PubMed 21734151 Fig. S2B to determine the location of this allele on the current reference sequence.