GORASP2

protein-coding

golgi reassembly stacking protein 2, the group of PDZ domain containing

Gene summary

This gene encodes a member of the Golgi reassembly stacking protein family. These proteins may play a role in the stacking of Golgi cisternae and Golgi ribbon formation, as well as Golgi fragmentation during apoptosis or mitosis. The encoded protein also plays a role in the intracellular transport of transforming growth factor alpha and may function as a molecular chaperone. A pseudogene of this gene is located on the short arm of chromosome 2. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]

MANE transcript

NM_015530.5

Inheritance

—

ClinVar variants

U:65B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr2:170,928,464-170,967,130

External References & Databases

Ensembl (ENSG00000115806)

Transcript & Mutation Effects

hg38 • Region Span ~38.7 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 GORASP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015530.5. 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
missense			62 clinvar	4 clinvar	1 clinvar	67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	65	4	2	71

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015530.5	RefSeq	NP_056345.3	10	MANE Select
ENST00000234160.5	Ensembl	ENSP00000234160.4	10	MANE Select
NM_001201428.2	RefSeq	NP_001188357.1	8	Standard
ENST00000442798.5	Ensembl	ENSP00000399889.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Golgi Cisternae Pericentriolar Stack Reorganization
Mitotic Prophase
M Phase
Cell Cycle
Cell Cycle, Mitotic

Biological Process

organelle organization
Golgi organization
spermatogenesis
cell differentiation
response to endoplasmic reticulum stress

Molecular Function

protein binding

Cellular Component

Golgi membrane
endoplasmic reticulum membrane
Golgi apparatus
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000234160
Coding exons: 10
Length: 38666
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125748
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.59	175	245	0.714	0.0000124	2865
Missense (PolyPhen)		23	44.994	0.51118		534
Synonymous	0.438	92	97.5	0.944	0.00000551	980
Loss of Function	3.55	3	20.2	0.148	0.00000116	236

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in the assembly and membrane stacking of the Golgi cisternae, and in the process by which Golgi stacks reform after breakdown during mitosis and meiosis (PubMed:10487747, PubMed:21515684, PubMed:22523075). May regulate the intracellular transport and presentation of a defined set of transmembrane proteins, such as transmembrane TGFA (PubMed:11101516). Required for normal acrosome formation during spermiogenesis and normal male fertility, probably by promoting colocalization of JAM2 and JAM3 at contact sites between germ cells and Sertoli cells (By similarity). {ECO:0000250|UniProtKB:Q99JX3, ECO:0000269|PubMed:10487747, ECO:0000269|PubMed:11101516, ECO:0000269|PubMed:21515684, ECO:0000269|PubMed:22523075}.;

Recessive Scores

pRec: 0.148

Intolerance Scores

LoFtool: 0.455
RVIS EVS: -0.27
RVIS percentile EVS: 34.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.817

Gene Damage Prediction

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