DEF8

differentially expressed in FDCP 8 homolog

Basic information

Region (hg38): 16:89948696-89968060

Links

ENSG00000140995 ∙ NCBI:54849 ∙ ∙ HGNC:25969 ∙ Uniprot:Q6ZN54 ∙ 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 DEF8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEF8 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					2	2
missense			25	4	1	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	1	1	7
Total	0	0	30	5	4

Variants in DEF8

This is a list of pathogenic ClinVar variants found in the DEF8 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-89949470-C-T		not specified	Likely benign (Aug 30, 2022)
16-89949498-C-T			Benign (Jun 27, 2018)
16-89949535-T-G		not specified	Uncertain significance (Dec 16, 2023)
16-89949564-G-C		not specified	Uncertain significance (Aug 02, 2022)
16-89949614-C-T		not specified	Uncertain significance (Sep 06, 2022)
16-89949626-C-A		not specified	Uncertain significance (Sep 16, 2021)
16-89949626-C-T		not specified	Uncertain significance (Nov 01, 2022)
16-89954283-C-T		not specified	Uncertain significance (Apr 24, 2023)
16-89954323-C-T		not specified	Uncertain significance (Jun 21, 2023)
16-89954337-C-G			Benign (Dec 20, 2018)
16-89954359-C-T		not specified	Likely benign (Apr 24, 2024)
16-89954364-G-A		not specified	Likely benign (Dec 17, 2021)
16-89954368-C-A		not specified	Uncertain significance (Nov 08, 2022)
16-89954370-C-T		not specified	Likely benign (Apr 25, 2022)
16-89955208-G-A		not specified	Likely benign (Feb 28, 2023)
16-89955219-C-T		not specified	Uncertain significance (May 31, 2023)
16-89955234-G-A		not specified	Uncertain significance (Nov 07, 2023)
16-89957589-G-A		not specified	Uncertain significance (Aug 09, 2021)
16-89957631-C-T		not specified	Uncertain significance (Dec 20, 2021)
16-89957637-C-T		not specified	Uncertain significance (Jul 26, 2022)
16-89957654-G-A			Benign (Dec 31, 2019)
16-89959021-A-G		not specified	Uncertain significance (Dec 27, 2023)
16-89959086-G-A		not specified	Uncertain significance (Dec 02, 2022)
16-89959153-C-G		not specified	Uncertain significance (May 01, 2024)
16-89960943-G-A		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEF8	protein_coding	protein_coding	ENST00000268676	12	20136

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00259	0.997	125723	0	22	125745	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	287	340	0.845	0.0000226	3319
Missense in Polyphen		62	97.669	0.63479		1040
Synonymous	-0.381	151	145	1.04	0.0000104	984
Loss of Function	3.35	10	29.7	0.336	0.00000166	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000870	0.0000870
Ashkenazi Jewish	0.000108	0.0000992
East Asian	0.000224	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000623	0.0000615
Middle Eastern	0.000224	0.000217
South Asian	0.000168	0.000163
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positively regulates lysosome peripheral distribution and ruffled border formation in osteoclasts. Involved in bone resorption. {ECO:0000250|UniProtKB:Q99J78}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.423
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.15

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.476
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.261

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Def8

Gene ontology

• Biological process: lysosome localization;intracellular signal transduction;positive regulation of bone resorption;positive regulation of ruffle assembly
• Molecular function: metal ion binding