FAM219A

family with sequence similarity 219 member A

Basic information

Region (hg38): 9:34398183-34458570

Previous symbols: [ "C9orf25" ]

Links

ENSG00000164970 ∙ NCBI:203259 ∙ ∙ HGNC:19920 ∙ Uniprot:Q8IW50 ∙ 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 FAM219A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM219A 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						0
missense			9			9
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	0	0

Variants in FAM219A

This is a list of pathogenic ClinVar variants found in the FAM219A region.

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

Position	Type	Phenotype	Significance	ClinVar
9-34401013-G-A		not specified	Uncertain significance (Aug 21, 2023)
9-34401683-C-T		not specified	Uncertain significance (Jun 07, 2023)
9-34402711-C-T		not specified	Uncertain significance (Feb 28, 2023)
9-34402723-T-C		not specified	Uncertain significance (Jan 23, 2023)
9-34402778-A-G		not specified	Uncertain significance (Jun 23, 2023)
9-34402798-C-T		not specified	Uncertain significance (Sep 16, 2021)
9-34405882-G-A		not specified	Uncertain significance (Oct 12, 2021)
9-34405946-T-C		not specified	Uncertain significance (Aug 30, 2021)
9-34405955-C-T		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM219A	protein_coding	protein_coding	ENST00000445726	6	60387

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.146	0.838	125737	0	7	125744	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.18	47	112	0.420	0.00000681	1208
Missense in Polyphen		19	57.366	0.33121		616
Synonymous	0.862	41	48.6	0.843	0.00000325	345
Loss of Function	2.07	3	10.1	0.297	5.15e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.380
• hipred: N
• hipred_score: 0.476
• ghis: 0.641

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Fam219a