FAM114A1

protein-coding

family with sequence similarity 114 member A1, the group of MicroRNA protein coding host genes

Gene summary

The protein encoded by this gene belongs to the FAM114 family and may play a role in neuronal cell development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2017]

MANE transcript

NM_138389.4

Inheritance

—

ClinVar variants

U:81B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.09

Max pathogenic AF

—

Genomic locus

chr4:38,867,677-38,945,739

External References & Databases

Ensembl (ENSG00000197712)

Transcript & Mutation Effects

hg38 • Region Span ~78.1 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 FAM114A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 77

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138389.4. 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			1 clinvar	1 clinvar		2
missense			76 clinvar	3 clinvar		79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	81	4	0	85

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138389.4	RefSeq	NP_612398.2	13	MANE Select
ENST00000358869.5	Ensembl	ENSP00000351740.2	13	MANE Select
NM_001330764.2	RefSeq	NP_001317693.1	10	Standard
NM_001350631.2	RefSeq	NP_001337560.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

nucleus
nucleoplasm
Golgi apparatus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358869
Coding exons: 13
Length: 78063
Individuals with no LoFs: 125546
Homozygous LoFs: 0
Heterozygous LoFs: 201
Defined: 125747
p: 0.000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.490	282	306	0.921	0.0000161	3654
Missense (PolyPhen)		91	111.67	0.81487		1263
Synonymous	-0.256	124	120	1.03	0.00000733	1084
Loss of Function	-0.429	29	26.6	1.09	0.00000112	366

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0010	0.00098	notable
Latino/Admixed American	0.0033	0.0032	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00035	0.00035	rare
South Asian	0.00085	0.00085	rare
Other	0.0012	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in neuronal cell development. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.837
RVIS EVS: 0.36
RVIS percentile EVS: 74.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.171

Gene Damage Prediction

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