FAM219A

protein-coding

family with sequence similarity 219 member A

Gene summary

The protein encoded by this gene has homologs that have been identified in mouse, macaque, etc organisms. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Dec 2010]

Previous symbols:

C9orf25

MANE transcript

NM_001184940.2

Inheritance

—

ClinVar variants

U:17

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr9:34,398,184-34,458,570

External References & Databases

Ensembl (ENSG00000164970)

Transcript & Mutation Effects

hg38 • Region Span ~60.4 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 FAM219A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001184940.2. 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						0
missense			15 clinvar			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	17	0	0	17

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001184940.2	RefSeq	NP_001171869.1	6	MANE Select
ENST00000651358.1	Ensembl	ENSP00000499069.1	6	MANE Select
NM_001184941.2	RefSeq	NP_001171870.1	6	Standard
NM_001184942.2	RefSeq	NP_001171871.1	6	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000445726
Coding exons: 6
Length: 60387
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125744
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.18	47	112	0.420	0.00000681	1208
Missense (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

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	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.101

Intolerance Scores

RVIS EVS: -0.01
RVIS percentile EVS: 52.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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