AJAP1

protein-coding

adherens junctions associated protein 1

Gene summary

Enables beta-catenin binding activity. Involved in negative regulation of cell-matrix adhesion; negative regulation of wound healing; and regulation of polarized epithelial cell differentiation. Located in several cellular components, including adherens junction; basolateral plasma membrane; and cell-cell contact zone. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018836.4

Inheritance

ClinVar variants

U:67B:4

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr1:4,654,609-4,792,534

External References & Databases

Ensembl (ENSG00000196581)

Transcript & Mutation Effects

hg38 • Region Span ~137.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AJAP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 61

not providedTotal: 7

AJAP1-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018836.4. 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			3
missense			63 clinvar	2 clinvar	2 clinvar	67
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	2	2	71

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018836.4	RefSeq	NP_061324.1	5	MANE Select
ENST00000378191.5	Ensembl	ENSP00000367433.3	5	MANE Select
NM_001042478.2	RefSeq	NP_001035943.1	5	Standard
ENST00000378190.7	Ensembl	ENSP00000367432.3	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of cell-matrix adhesion
cell adhesion
regulation of polarized epithelial cell differentiation
negative regulation of wound healing

Molecular Function

protein binding
beta-catenin binding
protein-containing complex binding

Cellular Component

cell-cell adherens junction
cytoplasmic side of plasma membrane
cell surface
basolateral plasma membrane
apical plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378191
Coding exons: 5
Length: 137803
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.936	200	241	0.830	0.0000161	2565
Missense (PolyPhen)		31	37.059	0.8365		354
Synonymous	0.163	106	108	0.980	0.00000793	889
Loss of Function	3.65	0	15.5	0.00	8.69e-7	154

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in cell adhesion and cell migration. {ECO:0000269|PubMed:16410724, ECO:0000269|PubMed:17267690}.;

Recessive Scores

pRec: 0.124

Intolerance Scores

RVIS EVS: 0.42
RVIS percentile EVS: 77.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.650

Gene Damage Prediction

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