FAM20A FAM20A golgi associated secretory pathway pseudokinase [Homo sapiens (human)] - Gene

Summary

Official Symbol: FAM20Aprovided by HGNC
Official Full Name: FAM20A golgi associated secretory pathway pseudokinaseprovided by HGNC
Primary source: HGNC:HGNC:23015
See related: Ensembl:ENSG00000108950 MIM:611062; AllianceGenome:HGNC:23015
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: AI1G; AIGFS; FP2747
Summary: This locus encodes a protein that is likely secreted and may function in hematopoiesis. A mutation at this locus has been associated with amelogenesis imperfecta and gingival hyperplasia syndrome. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Aug 2011]
Expression: Broad expression in salivary gland (RPKM 7.2), liver (RPKM 6.1) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q24.2

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (68535116..68601367, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (69411970..69478232, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (66531257..66597508, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

FAM20A-Associated Amelogenesis Imperfecta: Gene Variants with Functional Verification and Histological Features.
Title: FAM20A-Associated Amelogenesis Imperfecta: Gene Variants with Functional Verification and Histological Features.
FAM20A is a golgi-localized Type II transmembrane protein.
Title: FAM20A is a golgi-localized Type II transmembrane protein.
Deep dental phenotyping and a novel FAM20A variant in patients with amelogenesis imperfecta type IG.
Title: Deep dental phenotyping and a novel FAM20A variant in patients with amelogenesis imperfecta type IG.
FAM20A mutations and transcriptome analyses of dental pulp tissues of enamel renal syndrome.
Title: FAM20A mutations and transcriptome analyses of dental pulp tissues of enamel renal syndrome.
Two new families with enamel renal syndrome: A novel FAM20A gene mutation and review of literature.
Title: Two new families with enamel renal syndrome: A novel FAM20A gene mutation and review of literature.
Whole exome sequencing (WES) identified that Pt-1 was heterozygous for FAM20A, c.758A > G (p.Tyr253Cys), inherited from her father. The mutation on maternal allele was not detected by WES. Pt-2 possessed compound heterozygous mutations, c.1248dupG (p.Phe417Valfs*7); c.1081C > T (p.Arg361Cys) in FAM20A.
Title: Four novel mutations of FAM20A in amelogenesis imperfecta type IG and review of literature for its genotype and phenotype spectra.
Here we report the largest series of patients with Enamel renal syndrome in a same population, and describe, for the first time, a founder mutation for FAM20A.
Title: Enamel renal syndrome: A novel homozygous FAM20A founder mutation in 5 new Brazilian families.
Mutations in LAMB3 and FAM20A were found in 3 Turkish families with Amelogenesis imperfecta
Title: Candidate gene sequencing reveals mutations causing hypoplastic amelogenesis imperfecta.
Recessive FAM20A mutations can cause nephrocalcinosis in addition to the oral phenotype
Title: Nephrocalcinosis in Amelogenesis Imperfecta Caused by the FAM20A Mutation.
Physicochemical analysis of human pulpal mineralization secondary to FAM20A mutations.
Title: Physicochemical analysis of human pulpal mineralization secondary to FAM20A mutations.

Submit: New GeneRIF Correction See all GeneRIFs (21)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Amelogenesis imperfecta type 1G MedGen: C2931783 OMIM: 204690 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH46194 (e-PCR)
- UniSTS:9236

STS-W90672 (e-PCR)
- UniSTS:68928

SHGC-56444 (e-PCR)
- UniSTS:14964

FAM20A__7627 (e-PCR)
- UniSTS:471431

G20323 (e-PCR)
- UniSTS:79512

A005M04 (e-PCR)
- UniSTS:79513

D17S2193 (e-PCR), detects polymorphism
- UniSTS:68091

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
NOT enables phosphotransferase activity, alcohol group as acceptor	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein serine/threonine kinase activator activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein serine/threonine kinase activator activity	IDA Inferred from Direct Assay more info	PubMed
NOT enables protein serine/threonine kinase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in biomineral tissue development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcium ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in enamel mineralization	IBA Inferred from Biological aspect of Ancestor more info
involved_in enamel mineralization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in protein phosphorylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to bacterium	IEA Inferred from Electronic Annotation more info
involved_in tooth eruption	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
colocalizes_with Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
colocalizes_with Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: pseudokinase FAM20A

Names: family with sequence similarity 20, member A; protein FAM20A

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029809.1 RefSeqGene

Range

4588..70839

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001243746.2 → NP_001230675.1 pseudokinase FAM20A isoform b

See identical proteins and their annotated locations for NP_001230675.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate exon at its 5' end and uses a downstream start codon, compared to variant 1. The encoded protein (isoform b) has a shorter N-terminus compared to isoform a.

Source sequence(s)

AC079210, AK298071, AL133105, AY358197, BC036222

UniProtKB/TrEMBL

B7Z4Y3

Conserved Domains (1) summary

cd10469
Location:168 → 384

FAM20A_C; C-terminal putative kinase domain of FAM20A
NM_017565.4 → NP_060035.2 pseudokinase FAM20A isoform a precursor

See identical proteins and their annotated locations for NP_060035.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a).

Source sequence(s)

AC079210, AL133105, AY358197, BC036222, BC136686, CB530015, N64017

Consensus CDS

CCDS11679.1

UniProtKB/Swiss-Prot

B2RN47, B2RN49, Q96MK3, Q9UF95

UniProtKB/TrEMBL

L8B8N7

Related

ENSP00000468308.1, ENST00000592554.2

Conserved Domains (1) summary

cd10469
Location:306 → 522

FAM20A_C; C-terminal putative kinase domain of FAM20A

RNA

NR_027751.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) has multiple differences compared to variant 1. The transcript is sufficiently abundant to represent as a RefSeq record; however, the predicted protein is not represented because there is uncertainty about the protein-coding capacity of the transcript.

Source sequence(s)

AC079210, AL133105, BC036222, CB530015, DB057818, N64017

Related

ENST00000226094.9

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

68535116..68601367 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006721959.4 → XP_006722022.1 pseudokinase FAM20A isoform X1

See identical proteins and their annotated locations for XP_006722022.1

UniProtKB/TrEMBL

B7Z4Y3

Conserved Domains (1) summary

cd10469
Location:168 → 384

FAM20A_C; C-terminal putative kinase domain of FAM20A
XM_047436319.1 → XP_047292275.1 pseudokinase FAM20A isoform X3
XM_017024781.3 → XP_016880270.1 pseudokinase FAM20A isoform X2

Conserved Domains (1) summary

cl05973
Location:306 → 373

FAM20_C_like; C-terminal putative kinase domain of FAM20 (family with sequence similarity 20), Drosophila Four-jointed (Fj), and related proteins
XM_011524918.4 → XP_011523220.1 pseudokinase FAM20A isoform X4

Conserved Domains (1) summary

cl05973
Location:306 → 370

FAM20_C_like; C-terminal putative kinase domain of FAM20 (family with sequence similarity 20), Drosophila Four-jointed (Fj), and related proteins