FAM47A

Gene

family with sequence similarity 47 member A

Gene summary

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

MANE transcript

NM_203408.4

Inheritance

—

ClinVar variants

U:93B:28

Top phenotype

FAM47A-related disorder

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chrX:34,129,752-34,132,314

External References & Databases

Ensembl (ENSG00000185448)

Transcript & Mutation Effects

hg38 • Region Span ~2.6 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 FAM47A variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 102

not providedTotal: 14

FAM47A-related disorderTotal: 8

Intellectual disabilityTotal: 3

Abnormality of neuronal migrationTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_203408.4. 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				5 clinvar		5
missense			93 clinvar	17 clinvar	4 clinvar	114
nonsense						0
start loss				1 clinvar		1
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	93	24	4	121

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_203408.4	RefSeq	NP_981953.2	1	MANE Select
ENST00000346193.5	Ensembl	ENSP00000345029.3	1	MANE Select

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000346193
Coding exons: 1
Length: 2579

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0791	366	370	0.988	0.0000347	5104
Missense (PolyPhen)		156	168.32	0.92682		2626
Synonymous	-0.787	163	151	1.08	0.0000142	1677
Loss of Function

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	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

Intolerance Scores

LoFtool: 0.515
RVIS EVS: 1.22
RVIS percentile EVS: 93.24

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	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium