FAM222A

family with sequence similarity 222 member A

Basic information

Region (hg38): 12:109713825-109770495

Previous symbols: [ "C12orf34" ]

Links

ENSG00000139438 ∙ NCBI:84915 ∙ ∙ HGNC:25915 ∙ Uniprot:Q5U5X8 ∙ 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 FAM222A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM222A 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				2	4	6
missense		1	38			39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	38	2	4

Variants in FAM222A

This is a list of pathogenic ClinVar variants found in the FAM222A region.

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

Position	Type	Phenotype	Significance	ClinVar
12-109744189-C-T		not specified	Uncertain significance (Sep 23, 2023)
12-109744199-G-A		not specified	Uncertain significance (Dec 15, 2022)
12-109744202-C-G		not specified	Uncertain significance (Dec 06, 2024)
12-109744214-T-A		not specified	Uncertain significance (Aug 20, 2024)
12-109768012-G-A		not specified	Uncertain significance (Sep 06, 2022)
12-109768017-G-T		not specified	Uncertain significance (Sep 20, 2023)
12-109768032-A-G		not specified	Uncertain significance (Feb 14, 2023)
12-109768075-A-T		not specified	Uncertain significance (Jun 22, 2021)
12-109768131-C-T		not specified	Uncertain significance (Aug 15, 2023)
12-109768158-C-T		not specified	Uncertain significance (Dec 05, 2022)
12-109768167-A-G		not specified	Uncertain significance (Jul 02, 2024)
12-109768191-C-A		not specified	Uncertain significance (Oct 14, 2021)
12-109768212-C-T		not specified	Uncertain significance (Mar 21, 2023)
12-109768213-A-T		Abnormal brain morphology	Likely pathogenic (-)
12-109768214-C-G		not specified	Uncertain significance (Aug 15, 2023)
12-109768258-T-C		not specified	Uncertain significance (Oct 12, 2024)
12-109768293-G-A		not specified	Uncertain significance (Nov 09, 2024)
12-109768329-A-G		not specified	Uncertain significance (Feb 16, 2023)
12-109768347-G-A		not specified	Likely benign (Sep 26, 2024)
12-109768350-G-A		not specified	Uncertain significance (May 16, 2023)
12-109768366-C-T		not specified	Uncertain significance (Aug 21, 2024)
12-109768367-G-A			Benign (May 19, 2018)
12-109768398-T-G		not specified	Uncertain significance (Jun 03, 2024)
12-109768407-C-A		not specified	Uncertain significance (Sep 30, 2024)
12-109768425-C-T		not specified	Uncertain significance (May 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM222A	protein_coding	protein_coding	ENST00000538780	2	56280

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.851	0.148	123237	0	1	123238	0.00000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	246	301	0.818	0.0000204	2806
Missense in Polyphen		127	163.06	0.77885		1597
Synonymous	0.940	135	150	0.902	0.0000115	1031
Loss of Function	2.74	1	10.6	0.0940	4.52e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000546
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000546	0.0000546
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.369
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam222a