FAM83F

family with sequence similarity 83 member F, the group of Family with sequence similarity 83

Basic information

Region (hg38): 22:39994953-40043534

Links

ENSG00000133477 ∙ NCBI:113828 ∙ ∙ HGNC:25148 ∙ Uniprot:Q8NEG4 ∙ 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 FAM83F gene.

• Inborn genetic diseases (32 variants)
• Abnormal sperm morphology;Reduced sperm motility;Oligospermia (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM83F 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				1		1
missense			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	0

Variants in FAM83F

This is a list of pathogenic ClinVar variants found in the FAM83F region.

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

Position	Type	Phenotype	Significance	ClinVar
22-39995096-G-A			Likely benign (Jul 01, 2022)
22-39995113-C-T		not specified	Uncertain significance (Mar 14, 2023)
22-39995127-G-A		not specified	Uncertain significance (Nov 10, 2021)
22-39995160-G-C		not specified	Uncertain significance (Mar 21, 2023)
22-39995164-G-A		not specified	Uncertain significance (Jan 09, 2024)
22-39995265-G-A		not specified	Uncertain significance (Feb 13, 2024)
22-39995415-G-A		not specified	Uncertain significance (Oct 26, 2022)
22-39995443-G-A		not specified	Uncertain significance (Nov 30, 2022)
22-39995464-C-T		not specified	Uncertain significance (Apr 25, 2022)
22-39995490-C-T		not specified	Uncertain significance (Nov 19, 2022)
22-39995499-G-C		not specified	Uncertain significance (Dec 01, 2022)
22-40019168-G-T		not specified	Uncertain significance (Dec 03, 2021)
22-40019189-C-G		not specified	Uncertain significance (Aug 23, 2021)
22-40019207-A-G		not specified	Uncertain significance (Nov 18, 2022)
22-40019222-G-A		not specified	Uncertain significance (Dec 16, 2023)
22-40019231-G-A		not specified	Uncertain significance (May 18, 2023)
22-40019243-C-T		not specified	Uncertain significance (Jul 06, 2021)
22-40019327-C-T		not specified	Uncertain significance (Aug 08, 2022)
22-40019328-G-A		not specified	Uncertain significance (Apr 18, 2023)
22-40019894-G-A		not specified	Uncertain significance (Jun 28, 2022)
22-40019900-G-A		Abnormal sperm morphology;Oligospermia;Reduced sperm motility • not specified	Uncertain significance (Dec 03, 2021)
22-40019980-G-A		not specified	Uncertain significance (Jul 06, 2021)
22-40021304-C-G		not specified	Uncertain significance (Dec 26, 2023)
22-40021322-A-T		not specified	Uncertain significance (Sep 14, 2022)
22-40021358-C-G		not specified	Uncertain significance (Apr 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM83F	protein_coding	protein_coding	ENST00000333407	5	48581

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.76e-11	0.0614	125714	0	33	125747	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	254	307	0.828	0.0000193	3199
Missense in Polyphen		56	87.218	0.64207		1029
Synonymous	0.226	128	131	0.975	0.00000860	1041
Loss of Function	0.168	17	17.8	0.957	9.96e-7	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000700	0.000699
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.0000937	0.0000924
European (Non-Finnish)	0.0000989	0.0000967
Middle Eastern	0.000113	0.000109
South Asian	0.0000989	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.637
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.58

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.265
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.693

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam83f