FAM83H

family with sequence similarity 83 member H, the group of MicroRNA protein coding host genes|Family with sequence similarity 83

Basic information

Region (hg38): 8:143723933-143738234

Links

ENSG00000180921 ∙ NCBI:286077 ∙ OMIM:611927 ∙ HGNC:24797 ∙ Uniprot:Q6ZRV2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amelogenesis imperfecta, type 3A (Strong), mode of inheritance: AD
• amelogenesis imperfecta, type 3A (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amelogenesis imperfecta, type IIIA	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dental	18252228; 18484629; 19220331; 19407157; 21702852; 23355523

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM83H gene.

• Amelogenesis imperfecta, hypocalcification type (5 variants)
• Amelogenesis imperfecta, type 3A (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM83H 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				14	11	25
missense			126	10	15	151
nonsense	3	1				4
start loss						0
frameshift	2			1		3
inframe indel				1	1	2
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				1	5	6
Total	5	1	126	27	32

Variants in FAM83H

This is a list of pathogenic ClinVar variants found in the FAM83H region.

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

Position	Type	Phenotype	Significance	ClinVar
8-143725973-T-C		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
8-143726058-G-A		not specified	Uncertain significance (Mar 29, 2024)
8-143726063-T-C		Inborn genetic diseases	Uncertain significance (Aug 11, 2022)
8-143726102-A-T		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
8-143726109-G-A		Inborn genetic diseases	Uncertain significance (May 23, 2023)
8-143726123-G-A			Benign (Aug 16, 2018)
8-143726142-G-A			Uncertain significance (Dec 15, 2021)
8-143726160-T-C		Inborn genetic diseases	Uncertain significance (Oct 25, 2022)
8-143726168-C-A		Inborn genetic diseases	Uncertain significance (Jul 13, 2022)
8-143726178-G-A		Inborn genetic diseases	Uncertain significance (Apr 04, 2023)
8-143726189-G-A			Uncertain significance (Mar 25, 2023)
8-143726211-T-A		Inborn genetic diseases	Uncertain significance (Nov 02, 2023)
8-143726237-G-A		Inborn genetic diseases	Uncertain significance (Jan 07, 2022)
8-143726247-C-T		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)
8-143726250-G-C		FAM83H-related disorder	Likely benign (Mar 06, 2020)
8-143726267-G-T		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
8-143726268-T-G		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
8-143726269-C-T			Benign (Mar 29, 2018)
8-143726274-C-T		Inborn genetic diseases	Uncertain significance (Jan 05, 2022)
8-143726297-C-T		Inborn genetic diseases	Uncertain significance (Sep 01, 2021)
8-143726298-G-A		Inborn genetic diseases	Uncertain significance (Jul 20, 2022)
8-143726309-C-T		Inborn genetic diseases	Uncertain significance (Mar 06, 2023)
8-143726336-G-A		Inborn genetic diseases	Uncertain significance (Apr 10, 2023)
8-143726344-G-A			Benign (Jul 06, 2018)
8-143726375-T-G		Inborn genetic diseases	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM83H	protein_coding	protein_coding	ENST00000388913	4	9869

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.892	0.108	124352	0	435	124787	0.00174

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.417	824	791	1.04	0.0000623	7337
Missense in Polyphen		291	291.34	0.99882		2741
Synonymous	-2.10	440	387	1.14	0.0000341	2575
Loss of Function	4.16	5	29.3	0.171	0.00000160	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00125	0.00125
Ashkenazi Jewish	0.000894	0.000894
East Asian	0.000176	0.000167
Finnish	0.00116	0.00116
European (Non-Finnish)	0.00299	0.00299
Middle Eastern	0.000176	0.000167
South Asian	0.000392	0.000392
Other	0.00264	0.00264

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a major role in the structural organization and calcification of developing enamel (PubMed:18252228). May play a role in keratin cytoskeleton disassembly by recruiting CSNK1A1 to keratin filaments. Thereby, it may regulate epithelial cell migration (PubMed:23902688). {ECO:0000269|PubMed:18252228, ECO:0000269|PubMed:23902688}.

Recessive Scores

• pRec: 0.106

Haploinsufficiency Scores

• pHI: 0.274
• hipred: Y
• hipred_score: 0.622
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.661

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam83h
• Phenotype: skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: positive regulation of cell migration;biomineral tissue development;protein localization to cytoskeleton;intermediate filament cytoskeleton organization
• Cellular component: cytoplasm;keratin filament
• Molecular function: protein kinase binding;keratin filament binding