FAM83D

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

Basic information

Region (hg38): 20:38926312-38953106

Previous symbols: [ "C20orf129" ]

Links

ENSG00000101447 ∙ NCBI:81610 ∙ OMIM:618380 ∙ HGNC:16122 ∙ Uniprot:Q9H4H8 ∙ 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 FAM83D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM83D 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		2
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in FAM83D

This is a list of pathogenic ClinVar variants found in the FAM83D region.

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

Position	Type	Phenotype	Significance	ClinVar
20-38926539-C-A		not specified	Uncertain significance (Feb 22, 2023)
20-38926543-T-C		not specified	Uncertain significance (Dec 14, 2023)
20-38926766-G-C		not specified	Uncertain significance (Dec 22, 2023)
20-38947979-G-A		not specified	Uncertain significance (Mar 15, 2024)
20-38951747-C-T		not specified	Likely benign (Nov 17, 2022)
20-38951843-C-T		not specified	Uncertain significance (Sep 10, 2024)
20-38951850-G-A		not specified	Uncertain significance (May 20, 2024)
20-38951915-A-G		not specified	Uncertain significance (Feb 02, 2022)
20-38952021-C-T		not specified	Uncertain significance (Jan 18, 2025)
20-38952065-A-G		not specified	Uncertain significance (Jul 14, 2021)
20-38952252-T-A		not specified	Uncertain significance (Apr 20, 2024)
20-38952261-C-T		not specified	Uncertain significance (Mar 01, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM83D	protein_coding	protein_coding	ENST00000217429	4	26749

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.13e-8	0.531	124761	0	37	124798	0.000148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.214	320	331	0.967	0.0000173	3931
Missense in Polyphen		97	113.93	0.85143		1378
Synonymous	0.0377	140	141	0.996	0.00000758	1307
Loss of Function	1.02	14	18.8	0.746	0.00000104	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000323	0.000311
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000579	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000178	0.000177
Middle Eastern	0.0000579	0.0000556
South Asian	0.000301	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable proto-oncogene that regulates cell proliferation, growth, migration and epithelial to mesenchymal transition. Through the degradation of FBXW7, may act indirectly on the expression and downstream signaling of MTOR, JUN and MYC (PubMed:24344117). May play also a role in cell proliferation through activation of the ERK1/ERK2 signaling cascade (PubMed:25646692). May also be important for proper chromosome congression and alignment during mitosis through its interaction with KIF22. {ECO:0000269|PubMed:18485706, ECO:0000269|PubMed:24344117, ECO:0000269|PubMed:25646692}.

Intolerance Scores

• loftool: 0.827
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.663
• hipred: N
• hipred_score: 0.180
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.457

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam83d

Gene ontology

• Biological process: epithelial to mesenchymal transition;cell population proliferation;cell migration;regulation of TOR signaling;regulation of protein catabolic process;cell division;metaphase plate congression;regulation of ERK1 and ERK2 cascade;protein localization to mitotic spindle;positive regulation of cell cycle G1/S phase transition
• Cellular component: cytoplasm;mitotic spindle pole
• Molecular function: protein binding;microtubule binding;kinesin binding;protein kinase binding