WAPL

WAPL cohesin release factor, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 10:86435256-86521792

Previous symbols: [ "KIAA0261", "WAPAL" ]

Links

ENSG00000062650 ∙ NCBI:23063 ∙ OMIM:610754 ∙ HGNC:23293 ∙ Uniprot:Q7Z5K2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WAPL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WAPL gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			49			49
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	0	0

Variants in WAPL

This is a list of pathogenic ClinVar variants found in the WAPL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-86437967-T-C		not specified	Uncertain significance (Apr 23, 2024)
10-86443324-A-G		not specified	Uncertain significance (Nov 23, 2021)
10-86446384-A-T		not specified	Uncertain significance (Sep 14, 2022)
10-86446431-G-A		not specified	Uncertain significance (Dec 15, 2022)
10-86452001-C-T		not specified	Uncertain significance (Apr 05, 2023)
10-86452020-C-T		not specified	Uncertain significance (Jan 09, 2023)
10-86452037-A-G		not specified	Uncertain significance (Dec 16, 2023)
10-86452038-T-C		not specified	Uncertain significance (Nov 18, 2023)
10-86452058-G-C		not specified	Uncertain significance (Jan 22, 2024)
10-86452068-T-C		not specified	Uncertain significance (Jun 09, 2022)
10-86452070-T-C		not specified	Uncertain significance (Oct 02, 2023)
10-86452079-C-A		not specified	Uncertain significance (May 30, 2024)
10-86453718-T-G		not specified	Uncertain significance (May 14, 2024)
10-86453725-C-A		not specified	Uncertain significance (Dec 17, 2023)
10-86453790-C-T		not specified	Uncertain significance (Nov 18, 2022)
10-86460450-T-A		not specified	Uncertain significance (Dec 19, 2022)
10-86467457-C-T		WAPL-related disorder	Uncertain significance (Mar 08, 2018)
10-86467470-G-GTATA		not specified	Uncertain significance (Sep 14, 2022)
10-86472218-G-A		6 conditions	Uncertain significance (Dec 15, 2020)
10-86472674-T-A		not specified	Uncertain significance (Dec 08, 2023)
10-86472674-T-C		not specified	Uncertain significance (May 17, 2023)
10-86472692-C-T		not specified	Uncertain significance (May 15, 2024)
10-86472737-G-T		not specified	Uncertain significance (Feb 06, 2024)
10-86497263-T-C		not specified	Uncertain significance (Jun 18, 2021)
10-86497299-C-G		not specified	Uncertain significance (Apr 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WAPL	protein_coding	protein_coding	ENST00000298767	18	86560

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.27e-8	125720	0	2	125722	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.46	383	627	0.611	0.0000313	7915
Missense in Polyphen		80	260.94	0.30658		3276
Synonymous	1.04	199	218	0.911	0.0000108	2186
Loss of Function	6.72	2	56.5	0.0354	0.00000327	697

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of sister chromatid cohesion in mitosis which negatively regulates cohesin association with chromatin. Involved in both sister chromatid cohesion during interphase and sister- chromatid resolution during early stages of mitosis. Couples DNA replication to sister chromatid cohesion. Cohesion ensures that chromosome partitioning is accurate in both meiotic and mitotic cells and plays an important role in DNA repair. {ECO:0000269|PubMed:15150110, ECO:0000269|PubMed:17112726, ECO:0000269|PubMed:17113138, ECO:0000269|PubMed:19696148, ECO:0000269|PubMed:19907496, ECO:0000269|PubMed:21111234, ECO:0000269|PubMed:23776203}.
• Pathway: Establishment of Sister Chromatid Cohesion;S Phase;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;Cohesin Loading onto Chromatin;Mitotic Telophase/Cytokinesis;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• rvis_EVS: -1.2
• rvis_percentile_EVS: 5.83

Haploinsufficiency Scores

• pHI: 0.829
• hipred: Y
• hipred_score: 0.825
• ghis: 0.674

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Wapl
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype

Gene ontology

• Biological process: mitotic cell cycle;negative regulation of DNA replication;response to toxic substance;viral process;negative regulation of chromatin binding;meiotic chromosome segregation;negative regulation of sister chromatid cohesion;positive regulation of fibroblast proliferation;cell division;regulation of chromosome condensation;protein localization to chromatin;regulation of cohesin loading
• Cellular component: chromosome, centromeric region;chromatin;synaptonemal complex;nucleus;nucleoplasm;chromosome;cytoplasm;cytosol;cohesin complex
• Molecular function: protein binding