Human Gene Module / Chromosome 14 / ZFYVE26

ZFYVE26zinc finger FYVE-type containing 26

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
7 / 7
Rare Variants / Common Variants
9 / 0
Aliases
ZFYVE26, FYVE-CENT,  SPG15
Associated Syndromes
-
Chromosome Band
14q24.1
Associated Disorders
-
Relevance to Autism

A de novo frameshift variant and two de novo missense variants that were predicted to be damaging (CADD score > 30) were identified in ASD probands from the Autism Sequencing Consortium and the Simons Simplex Collection (De Rubeis et al., 2014; Iossifov et al., 2014). TADA analysis of 4,504 ASD trios and 3,012 unaffected control/siblings trios from trio-based exome/genome sequencing studies identified ZFYVE26 as an ASD candidate gene with a q-value < 0.1 (Du et al., 2019).

Molecular Function

This gene encodes a protein which contains a FYVE zinc finger binding domain. The presence of this domain is thought to target these proteins to membrane lipids through interaction with phospholipids in the membrane. Mutations in this gene are associated with autosomal recessive spastic paraplegia-15.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneOMIMUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to ZFYVE26 (7 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Synaptic, transcriptional and chromatin genes disrupted in autism De Rubeis S , et al. (2014) Yes -
2 Support The contribution of de novo coding mutations to autism spectrum disorder Iossifov I et al. (2014) Yes -
3 Recent Recommendation Nonrandom occurrence of multiple de novo coding variants in a proband indicates the existence of an oligogenic model in autism Du Y , et al. (2019) Yes -
4 Support Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks Ruzzo EK , et al. (2019) Yes -
5 Support - Woodbury-Smith M et al. (2022) Yes -
6 Support - Zhou X et al. (2022) Yes -
7 Support - Cirnigliaro M et al. (2023) Yes -
Rare Variants   (9)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.3450C>T p.Asp1150%3D synonymous_variant De novo - - 35982159 Zhou X et al. (2022)
c.5173G>A p.Ala1725Thr missense_variant De novo - - 25363760 De Rubeis S , et al. (2014)
c.4548G>A p.Ala1516%3D synonymous_variant De novo - Simplex 35982159 Zhou X et al. (2022)
c.1311C>A p.His437Gln missense_variant Unknown - - 35205252 Woodbury-Smith M et al. (2022)
c.6248G>A p.Arg2083Gln missense_variant De novo - Simplex 25363768 Iossifov I et al. (2014)
c.1128C>T p.His376%3D synonymous_variant Unknown - - 35205252 Woodbury-Smith M et al. (2022)
c.1017+1G>T - splice_site_variant Familial Maternal Multiplex 37506195 Cirnigliaro M et al. (2023)
c.1190del p.Gly397AlafsTer93 frameshift_variant De novo - Simplex 25363768 Iossifov I et al. (2014)
c.1201_1210del p.Leu401MetfsTer86 frameshift_variant Familial Paternal Multiplex 31398340 Ruzzo EK , et al. (2019)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

A de novo frameshift variant and two de novo missense variants that were predicted to be damaging (CADD score > 30) were identified in ASD probands from the Autism Sequencing Consortium and the Simons Simplex Collection (De Rubeis et al., 2014; Iossifov et al., 2014). TADA analysis of 4,504 ASD trios and 3,012 unaffected control/siblings trios from trio-based exome/genome sequencing studies identified ZFYVE26 as an ASD candidate gene with a q-value < 0.1 (Du et al., 2019).

Score Delta: Score remained at 2

criteria met
See SFARI Gene'scoring criteria
2

Strong Candidate

See all Category 2 Genes

We considered a rigorous statistical comparison between cases and controls, yielding genome-wide statistical significance, with independent replication, to be the strongest possible evidence for a gene. These criteria were relaxed slightly for category 2.

4/1/2022
3
icon
2

Decreased from 3 to 2

Description

A de novo frameshift variant and two de novo missense variants that were predicted to be damaging (CADD score > 30) were identified in ASD probands from the Autism Sequencing Consortium and the Simons Simplex Collection (De Rubeis et al., 2014; Iossifov et al., 2014). TADA analysis of 4,504 ASD trios and 3,012 unaffected control/siblings trios from trio-based exome/genome sequencing studies identified ZFYVE26 as an ASD candidate gene with a q-value < 0.1 (Du et al., 2019).

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

A de novo frameshift variant and two de novo missense variants that were predicted to be damaging (CADD score > 30) were identified in ASD probands from the Autism Sequencing Consortium and the Simons Simplex Collection (De Rubeis et al., 2014; Iossifov et al., 2014). TADA analysis of 4,504 ASD trios and 3,012 unaffected control/siblings trios from trio-based exome/genome sequencing studies identified ZFYVE26 as an ASD candidate gene with a q-value < 0.1 (Du et al., 2019).

Reports Added
[New Scoring Scheme]
7/1/2019
icon
4

Increased from to 4

Description

A de novo frameshift variant and two de novo missense variants that were predicted to be damaging (CADD score > 30) were identified in ASD probands from the Autism Sequencing Consortium and the Simons Simplex Collection (De Rubeis et al., 2014; Iossifov et al., 2014). TADA analysis of 4,504 ASD trios and 3,012 unaffected control/siblings trios from trio-based exome/genome sequencing studies identified ZFYVE26 as an ASD candidate gene with a q-value < 0.1 (Du et al., 2019).

Krishnan Probability Score

Score 0.43472005610972

Ranking 20504/25841 scored genes


[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning approach on a human brain-specific gene network. The method was first presented in Nat Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed in column G of supplementary table 3 (see: http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at asd.princeton.edu.
Original Source
ExAC Score

Score 1.0384457260296E-11

Ranking 17167/18225 scored genes


[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of- function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of- function mutations in autism in such a gene would be more likely to confer risk. For a full list of pLI scores see: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle aned_exac_nonTCGA_z_pli_rec_null_data.txt
Original Source
Sanders TADA Score

Score 0.43178062096833

Ranking 323/18665 scored genes


[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013), and is a statistic that integrates evidence from both de novo and transmitted mutations. It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233 (2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper (the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Original Source
Zhang D Score

Score 0.29504986220275

Ranking 2822/20870 scored genes


[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures), or D score, was developed to combine evidence from de novo loss-of- function mutation with evidence from cell-type- specific gene expression in the mouse brain (specifically translational profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with positive D scores are more likely to be associated with autism risk, with higher-confidence genes having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204- 215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in supplementary table 2 from that paper.
Original Source
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