AFAP1

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

Basic information

Region (hg38): 4:7758714-7939926

Links

ENSG00000196526 ∙ NCBI:60312 ∙ OMIM:608252 ∙ HGNC:24017 ∙ Uniprot:Q8N556 ∙ 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 AFAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AFAP1 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				3	2	5
missense			78	3		81
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	78	6	2

Variants in AFAP1

This is a list of pathogenic ClinVar variants found in the AFAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-7763774-G-A			Likely benign (May 01, 2023)
4-7763778-T-C		not specified	Uncertain significance (Sep 12, 2023)
4-7768866-C-T		not specified	Uncertain significance (Dec 18, 2023)
4-7768873-A-T		not specified	Uncertain significance (Aug 03, 2021)
4-7768876-G-A		not specified	Uncertain significance (Nov 09, 2024)
4-7768888-G-A		not specified	Uncertain significance (Dec 15, 2023)
4-7768890-G-A		not specified	Uncertain significance (Jun 16, 2023)
4-7768912-C-T		not specified	Uncertain significance (Mar 06, 2023)
4-7768913-G-A			Likely benign (Sep 01, 2022)
4-7768917-G-A		not specified	Uncertain significance (Jun 11, 2021)
4-7772841-C-G		not specified	Uncertain significance (Oct 10, 2023)
4-7772855-C-A		not specified	Uncertain significance (Aug 16, 2021)
4-7772855-C-T		not specified	Uncertain significance (Jun 26, 2024)
4-7772873-C-G		not specified	Uncertain significance (Apr 18, 2023)
4-7772884-G-A		not specified	Uncertain significance (Nov 23, 2024)
4-7772896-C-T		not specified	Uncertain significance (May 14, 2024)
4-7772906-C-T		not specified	Uncertain significance (Oct 12, 2024)
4-7772911-G-A		not specified	Uncertain significance (Apr 20, 2024)
4-7772941-G-A		not specified	Uncertain significance (Oct 04, 2022)
4-7772954-G-A		not specified	Uncertain significance (Apr 07, 2022)
4-7772958-C-T			Benign (May 24, 2018)
4-7772971-T-C		not specified	Likely benign (Mar 24, 2023)
4-7772980-T-C		not specified	Uncertain significance (Aug 02, 2021)
4-7772982-C-G		not specified	Likely benign (Feb 27, 2024)
4-7772995-G-A		not specified	Likely benign (Oct 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AFAP1	protein_coding	protein_coding	ENST00000420658	17	181213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.38e-7	1.00	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.909	558	501	1.11	0.0000316	5260
Missense in Polyphen		166	173.4	0.95732		1798
Synonymous	-3.01	277	220	1.26	0.0000156	1624
Loss of Function	3.24	18	40.1	0.448	0.00000194	492

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000302	0.000302
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000150	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can cross-link actin filaments into both network and bundle structures (By similarity). May modulate changes in actin filament integrity and induce lamellipodia formation. May function as an adapter molecule that links other proteins, such as SRC and PKC to the actin cytoskeleton. Seems to play a role in the development and progression of prostate adenocarcinoma by regulating cell-matrix adhesions and migration in the cancer cells. {ECO:0000250, ECO:0000269|PubMed:15485829}.

Intolerance Scores

• loftool: 0.473
• rvis_EVS: -1.96
• rvis_percentile_EVS: 1.84

Haploinsufficiency Scores

• pHI: 0.147
• hipred: Y
• hipred_score: 0.544
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.778

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Afap1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of signal transduction;regulation of cytoskeleton organization
• Cellular component: cytosol;focal adhesion;actin cytoskeleton
• Molecular function: actin binding