AFAP1L2

actin filament associated protein 1 like 2, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 10:114294823-114404756

Previous symbols: [ "KIAA1914" ]

Links

ENSG00000169129 ∙ NCBI:84632 ∙ OMIM:612420 ∙ HGNC:25901 ∙ Uniprot:Q8N4X5 ∙ 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 AFAP1L2 gene.

• Inborn genetic diseases (48 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AFAP1L2 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				4	1	5
missense			48			48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	4	1

Variants in AFAP1L2

This is a list of pathogenic ClinVar variants found in the AFAP1L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-114296052-C-T		not specified	Uncertain significance (Dec 06, 2021)
10-114297016-C-T		not specified	Likely benign (Jan 09, 2024)
10-114297021-G-A		not specified	Uncertain significance (Aug 11, 2022)
10-114297036-T-C		not specified	Uncertain significance (Apr 25, 2023)
10-114297070-C-A		not specified	Uncertain significance (Dec 19, 2022)
10-114297241-G-A			Likely benign (Jan 01, 2023)
10-114297243-G-T		not specified	Uncertain significance (Jan 23, 2023)
10-114297258-T-C		not specified	Uncertain significance (Aug 05, 2023)
10-114297275-G-A		not specified	Uncertain significance (May 11, 2022)
10-114297289-C-G		not specified	Uncertain significance (Apr 11, 2023)
10-114297290-T-C		not specified	Uncertain significance (Mar 22, 2023)
10-114297337-G-A			Benign/Likely benign (Mar 01, 2023)
10-114297339-G-A		not specified	Uncertain significance (Aug 10, 2021)
10-114297351-C-T		not specified	Uncertain significance (Sep 30, 2021)
10-114297357-G-A		not specified	Uncertain significance (Dec 22, 2023)
10-114297366-C-T		not specified	Uncertain significance (Feb 11, 2022)
10-114297389-T-C		not specified	Uncertain significance (Sep 12, 2023)
10-114297398-G-A		not specified	Uncertain significance (Jul 09, 2021)
10-114300208-C-T		not specified	Uncertain significance (Oct 26, 2021)
10-114300246-G-C			Likely benign (Aug 01, 2022)
10-114300314-C-T		not specified	Uncertain significance (Apr 19, 2023)
10-114300356-C-T		not specified	Uncertain significance (Jan 11, 2023)
10-114300551-G-C		not specified	Uncertain significance (Mar 01, 2023)
10-114300555-G-A		not specified	Uncertain significance (Jun 06, 2023)
10-114300578-C-T		not specified	Uncertain significance (May 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AFAP1L2	protein_coding	protein_coding	ENST00000304129	19	109933

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00216	0.998	125699	1	48	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.654	429	469	0.915	0.0000273	5321
Missense in Polyphen		123	141.12	0.87159		1670
Synonymous	-0.0213	201	201	1.00	0.0000128	1589
Loss of Function	4.19	13	42.5	0.306	0.00000199	516

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000424	0.000423
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000237	0.000231
European (Non-Finnish)	0.000191	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.000393	0.000359
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in a signaling cascade by enhancing the kinase activity of SRC. Contributes to SRC-regulated transcription activation. {ECO:0000269|PubMed:17412687}.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.636
• rvis_EVS: 0.79
• rvis_percentile_EVS: 87.3

Haploinsufficiency Scores

• pHI: 0.266
• hipred: Y
• hipred_score: 0.540
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.196

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Afap1l2
• 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); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: inflammatory response;regulation of mitotic cell cycle;regulation of interleukin-6 production;positive regulation of interleukin-8 production;positive regulation of epidermal growth factor receptor signaling pathway;positive regulation of transcription, DNA-templated;positive regulation of protein tyrosine kinase activity
• Cellular component: cytoplasm;cytosol;plasma membrane
• Molecular function: SH3 domain binding;protein tyrosine kinase activator activity;signaling adaptor activity;SH2 domain binding