AFAP1L1

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

Basic information

Region (hg38): 5:149271858-149343637

Links

ENSG00000157510 ∙ NCBI:134265 ∙ OMIM:614410 ∙ HGNC:26714 ∙ Uniprot:Q8TED9 ∙ 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 AFAP1L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AFAP1L1 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			43			43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	0	0

Variants in AFAP1L1

This is a list of pathogenic ClinVar variants found in the AFAP1L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-149299560-A-G		not specified	Uncertain significance (Dec 13, 2023)
5-149299578-C-T		not specified	Uncertain significance (Dec 21, 2023)
5-149299596-T-C		not specified	Uncertain significance (Jun 17, 2022)
5-149300300-A-C		not specified	Uncertain significance (May 30, 2024)
5-149301151-T-A		not specified	Uncertain significance (Apr 17, 2023)
5-149301189-G-A		not specified	Uncertain significance (May 23, 2023)
5-149301220-G-T		not specified	Uncertain significance (Oct 14, 2023)
5-149302437-C-T		not specified	Uncertain significance (Jun 05, 2023)
5-149302452-C-T		not specified	Uncertain significance (Apr 16, 2024)
5-149302457-C-T		not specified	Uncertain significance (Apr 24, 2024)
5-149302496-G-A		not specified	Uncertain significance (Apr 07, 2022)
5-149302508-G-A		not specified	Uncertain significance (Nov 21, 2022)
5-149302514-A-G		not specified	Uncertain significance (Oct 10, 2023)
5-149306327-C-T		not specified	Uncertain significance (May 01, 2022)
5-149306380-G-A		not specified	Likely benign (Apr 04, 2024)
5-149306389-G-A		not specified	Uncertain significance (Dec 22, 2023)
5-149307486-A-C		not specified	Uncertain significance (Oct 06, 2021)
5-149307561-G-A		not specified	Uncertain significance (Dec 16, 2023)
5-149307612-T-C		not specified	Uncertain significance (Jan 03, 2024)
5-149310121-G-A		not specified	Uncertain significance (Oct 04, 2022)
5-149312119-G-A		not specified	Uncertain significance (Dec 20, 2023)
5-149312173-C-T		not specified	Uncertain significance (Oct 16, 2023)
5-149312178-C-T		not specified	Uncertain significance (May 17, 2023)
5-149315896-C-T		not specified	Uncertain significance (Mar 11, 2024)
5-149316223-G-A		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AFAP1L1	protein_coding	protein_coding	ENST00000296721	19	69932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.96e-14	0.925	125651	0	97	125748	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	399	461	0.865	0.0000284	4965
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000696	0.000695
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.000103	0.0000924
European (Non-Finnish)	0.000429	0.000422
Middle Eastern	0.000163	0.000163
South Asian	0.000957	0.000915
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0962
• hipred: N
• hipred_score: 0.466
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.570

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Afap1l1

Gene ontology

• Cellular component: podosome;cytoplasm;cell junction;invadopodium
• Molecular function: protein binding