FAM200C

family with sequence similarity 200 member C

Basic information

Region (hg38): 5:160393148-160400054

Previous symbols: [ "C5orf54", "ZBED8" ]

Links

ENSG00000221886 ∙ NCBI:63920 ∙ OMIM:615253 ∙ HGNC:30804 ∙ Uniprot:Q8IZ13 ∙ 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 FAM200C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM200C 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	1

Variants in FAM200C

This is a list of pathogenic ClinVar variants found in the FAM200C region.

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

Position	Type	Phenotype	Significance	ClinVar
5-160394996-G-T			Benign (Jan 30, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM200C	protein_coding	protein_coding	ENST00000408953	1	6950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000266	0.931	124362	1	166	124529	0.000671

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0703	305	308	0.989	0.0000155	3974
Missense in Polyphen		83	90.539	0.91673		1149
Synonymous	-0.287	116	112	1.03	0.00000576	1111
Loss of Function	1.69	10	17.7	0.566	0.00000103	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00227	0.00226
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000286	0.000277
European (Non-Finnish)	0.000695	0.000683
Middle Eastern	0.000272	0.000272
South Asian	0.000131	0.000131
Other	0.000986	0.000980

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.61

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.299
• ghis: 0.541

Essentials

• essential_gene_gene_trap: N

Gene ontology

• Cellular component: nucleoplasm
• Molecular function: protein binding