ZPLD1

zona pellucida like domain containing 1

Basic information

Region (hg38): 3:102099243-102479841

Links

ENSG00000170044 ∙ NCBI:131368 ∙ OMIM:615915 ∙ HGNC:27022 ∙ Uniprot:Q8TCW7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZPLD1 gene.

• Inborn genetic diseases (13 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZPLD1 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	13	0	1

Variants in ZPLD1

This is a list of pathogenic ClinVar variants found in the ZPLD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-102438490-G-A		not specified	Uncertain significance (Feb 12, 2024)
3-102438554-G-A		not specified	Uncertain significance (Mar 17, 2023)
3-102452933-A-G		not specified	Uncertain significance (Mar 02, 2023)
3-102453122-T-C		not specified	Uncertain significance (Jan 02, 2024)
3-102456248-G-A		not specified	Uncertain significance (Sep 12, 2023)
3-102456283-C-T		not specified	Uncertain significance (Jun 24, 2022)
3-102456362-C-A		not specified	Uncertain significance (Jun 09, 2022)
3-102464205-C-T		not specified	Uncertain significance (Apr 01, 2022)
3-102464227-A-G		not specified	Uncertain significance (May 11, 2022)
3-102464242-T-C		not specified	Uncertain significance (Feb 26, 2024)
3-102468964-C-T		not specified	Likely benign (Feb 05, 2024)
3-102469062-A-G		not specified	Uncertain significance (May 08, 2023)
3-102469122-C-A		not specified	Uncertain significance (Jan 04, 2024)
3-102470398-G-A		not specified	Uncertain significance (Nov 30, 2022)
3-102470434-C-T		not specified	Uncertain significance (Nov 03, 2023)
3-102470467-C-G		not specified	Uncertain significance (Jul 19, 2022)
3-102477003-T-A			Benign (May 25, 2018)
3-102477020-C-G		not specified	Uncertain significance (Oct 25, 2023)
3-102477443-G-T		not specified	Uncertain significance (Apr 28, 2022)
3-102477469-C-G		not specified	Uncertain significance (Oct 12, 2021)
3-102477568-G-C		not specified	Uncertain significance (Apr 25, 2022)
3-102477605-C-G		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZPLD1	protein_coding	protein_coding	ENST00000306176	11	380598

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.45e-8	0.830	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.242	251	240	1.04	0.0000124	2822
Missense in Polyphen		57	70.18	0.8122		859
Synonymous	-1.09	101	88.0	1.15	0.00000483	828
Loss of Function	1.53	15	22.9	0.654	0.00000131	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.000109	0.000109
South Asian	0.0000681	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycoprotein which is a component of the gelatinous extracellular matrix in the cupulae of the vestibular organ. {ECO:0000250|UniProtKB:C0H9B6}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.365
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.92

Haploinsufficiency Scores

• pHI: 0.225
• hipred: N
• hipred_score: 0.331
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.105

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Zpld1

Gene ontology

• Cellular component: extracellular region;integral component of membrane;cytoplasmic vesicle membrane