AFAP1L1

protein-coding

actin filament associated protein 1 like 1, the group of Pleckstrin homology domain containing

Gene summary

Predicted to be located in cytoplasm; podosome; and stress fiber. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_152406.4

Inheritance

—

ClinVar variants

U:134B:2

Top phenotype

Neuromuscular disease

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr5:149,271,859-149,343,637

External References & Databases

Ensembl (ENSG00000157510)

Transcript & Mutation Effects

hg38 • Region Span ~71.8 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 AFAP1L1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 129

Neuromuscular diseaseTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152406.4. 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						0
missense			132 clinvar	2 clinvar		134
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	134	2	0	136

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152406.4	RefSeq	NP_689619.1	19	MANE Select
ENST00000296721.9	Ensembl	ENSP00000296721.4	19	MANE Select
NM_001146337.3	RefSeq	NP_001139809.1	18	Standard
NM_001323062.2	RefSeq	NP_001309991.1	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

podosome
cytoplasm
cell junction
invadopodium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296721
Coding exons: 19
Length: 69932
Individuals with no LoFs: 125651
Homozygous LoFs: 0
Heterozygous LoFs: 97
Defined: 125748
p: 0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.03	399	461	0.865	0.0000284	4965
Missense (PolyPhen)		137	162.14	0.84497		1805
Synonymous	0.713	178	191	0.934	0.0000120	1500
Loss of Function	2.16	28	43.3	0.647	0.00000237	500

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0.00010	0.000092	rare
European (Non-Finnish)	0.00043	0.00042	rare
South Asian	0.00096	0.00091	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in podosome and invadosome formation. {ECO:0000269|PubMed:21333378}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.763
RVIS EVS: -0.12
RVIS percentile EVS: 44.1

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.570

Gene Damage Prediction

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