ZPLD1

protein-coding

zona pellucida like domain containing 1

Gene summary

Predicted to act upstream of or within vestibular reflex. Predicted to be located in cytoplasmic vesicle membrane. Predicted to be active in cell surface and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001329788.2

Inheritance

—

ClinVar variants

U:59B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr3:102,099,244-102,479,841

External References & Databases

Ensembl (ENSG00000170044)

Transcript & Mutation Effects

hg38 • Region Span ~380.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZPLD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 59

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001329788.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	1 clinvar		4
missense			55 clinvar	3 clinvar		58
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	59	4	0	63

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001329788.2	RefSeq	NP_001316717.1	10	MANE Select
ENST00000466937.2	Ensembl	ENSP00000418253.1	10	MANE Select
NM_175056.2	RefSeq	NP_778226.1	11	Standard
ENST00000306176.5	Ensembl	ENSP00000307801.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular region
integral component of membrane
cytoplasmic vesicle membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000306176
Coding exons: 11
Length: 380598
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 36
Defined: 125748
p: 0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.242	251	240	1.04	0.0000124	2822
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00023	0.00023	rare
South Asian	0.000068	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.105

Gene Damage Prediction

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