FAM222A

Gene

family with sequence similarity 222 member A

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

C12orf34

MANE transcript

NM_032829.3

Inheritance

—

ClinVar variants

P:1U:96B:12

Top phenotype

Abnormal brain morphology

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr12:109,713,825-109,770,495

External References & Databases

Ensembl (ENSG00000139438)

Transcript & Mutation Effects

hg38 • Region Span ~56.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAM222A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 98

not providedTotal: 8

Abnormal brain morphologyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032829.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	4 clinvar	8
missense		1 clinvar	95 clinvar	4 clinvar		100
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	96	8	4	109

Highest pathogenic variant AF is 0.00001550253

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032829.3	RefSeq	NP_116218.2	2	MANE Select
ENST00000538780.2	Ensembl	ENSP00000443292.1	2	MANE Select
ENST00000358906.3	Ensembl	ENSP00000351783.3	2	Standard
ENST00000358906.4	Ensembl	ENSP00000351783.3	2	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000538780
Coding exons: 2
Length: 56280
Individuals with no LoFs: 123237
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 123238
p: 0.00000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.12	246	301	0.818	0.0000204	2806
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000055	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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