FAM83F

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

Basic information

Region (hg38): 22:39994954-40043534

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.

• not_specified (84 variants)
• not_provided (1 variants)
• Abnormal_sperm_morphology (1 variants)
• Reduced_sperm_motility (1 variants)
• Oligospermia (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. These statistics are base on transcript: NM_000138435.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			82	2		84
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	82	3	0

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