AVL9

AVL9 cell migration associated, the group of DENN domain containing

Basic information

Region (hg38): 7:32495425-32588726

Previous symbols: [ "KIAA0241" ]

Links

ENSG00000105778 ∙ NCBI:23080 ∙ OMIM:612927 ∙ HGNC:28994 ∙ Uniprot:Q8NBF6 ∙ 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 AVL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AVL9 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			30	3		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	3	0

Variants in AVL9

This is a list of pathogenic ClinVar variants found in the AVL9 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-32495726-G-T		not specified	Uncertain significance (Mar 15, 2024)
7-32495744-C-A		not specified	Uncertain significance (Dec 13, 2023)
7-32495752-C-G		not specified	Uncertain significance (Dec 18, 2023)
7-32495792-A-G		not specified	Uncertain significance (Aug 10, 2023)
7-32543159-C-G		not specified	Uncertain significance (Jun 19, 2024)
7-32543196-T-C		not specified	Uncertain significance (Feb 03, 2023)
7-32544760-A-T		not specified	Uncertain significance (Jul 30, 2023)
7-32548860-G-A		not specified	Uncertain significance (Aug 16, 2021)
7-32551335-C-G		not specified	Uncertain significance (Sep 15, 2021)
7-32551377-A-G		not specified	Uncertain significance (Feb 12, 2024)
7-32552259-G-A		not specified	Uncertain significance (Apr 12, 2022)
7-32553757-T-G		not specified	Uncertain significance (Oct 27, 2022)
7-32554594-A-G		not specified	Uncertain significance (Jan 08, 2024)
7-32558974-G-A		not specified	Uncertain significance (Dec 22, 2023)
7-32559010-G-T		not specified	Uncertain significance (Feb 22, 2023)
7-32559058-C-T		not specified	Uncertain significance (Jan 18, 2022)
7-32559078-A-G		not specified	Likely benign (May 15, 2023)
7-32559178-A-G		not specified	Likely benign (Oct 03, 2023)
7-32559226-C-T		not specified	Uncertain significance (Apr 08, 2024)
7-32559234-A-T		not specified	Uncertain significance (Aug 12, 2021)
7-32559309-C-A		not specified	Uncertain significance (Nov 08, 2021)
7-32559328-A-G		not specified	Uncertain significance (Aug 15, 2023)
7-32570042-T-C		not specified	Uncertain significance (Jun 22, 2023)
7-32570077-A-G		not specified	Uncertain significance (Jul 20, 2021)
7-32573206-A-C		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AVL9	protein_coding	protein_coding	ENST00000318709	16	543479

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00263	0.997	125707	0	40	125747	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	271	337	0.805	0.0000169	4223
Missense in Polyphen		86	126.83	0.67808		1560
Synonymous	-0.176	127	125	1.02	0.00000662	1249
Loss of Function	3.67	11	34.2	0.322	0.00000171	422

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.000120	0.000109
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.000249	0.000246
Middle Eastern	0.000120	0.000109
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions in cell migration. {ECO:0000269|PubMed:22595670}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.31

Haploinsufficiency Scores

• pHI: 0.209
• hipred: N
• hipred_score: 0.475
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.232

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Avl9

Gene ontology

• Biological process: cell migration
• Cellular component: integral component of membrane;recycling endosome