GULP1

protein-coding

GULP PTB domain containing engulfment adaptor 1, the group of MicroRNA protein coding host genes

Gene summary

The protein encoded by this gene is an adapter protein necessary for the engulfment of apoptotic cells by phagocytes. Several transcript variants, some protein coding and some thought not to be protein coding, have been found for this gene. [provided by RefSeq, Nov 2011]

MANE transcript

NM_016315.4

Inheritance

—

ClinVar variants

U:30B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr2:188,291,669-188,595,931

External References & Databases

Ensembl (ENSG00000144366)

Transcript & Mutation Effects

hg38 • Region Span ~304.3 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 GULP1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 27

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016315.4. 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
missense			26 clinvar	1 clinvar		27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	30	1	0	31

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 276 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016315.4	RefSeq	NP_057399.1	10	MANE Select
ENST00000409830.6	Ensembl	ENSP00000386732.1	10	MANE Select
NM_001252668.2	RefSeq	NP_001239597.1	11	Standard
NM_001252669.2	RefSeq	NP_001239598.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Arf6 signaling events

Biological Process

lipid transport
phagocytosis, engulfment
apoptotic process

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409580
Coding exons: 10
Length: 304258
Individuals with no LoFs: 125710
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125720
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.983	122	157	0.779	0.00000746	2010
Missense (PolyPhen)		34	58.038	0.58582		818
Synonymous	0.718	47	53.7	0.875	0.00000277	540
Loss of Function	3.13	3	16.9	0.178	7.10e-7	232

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000066	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.000069	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as an adapter protein. Required for efficient phagocytosis of apoptotic cells. Modulates cellular glycosphingolipid and cholesterol transport. May play a role in the internalization and endosomal trafficking of various LRP1 ligands, such as PSAP. Increases cellular levels of GTP-bound ARF6. {ECO:0000269|PubMed:10574763, ECO:0000269|PubMed:10574771, ECO:0000269|PubMed:16497666, ECO:0000269|PubMed:17398097}.;

Recessive Scores

pRec: 0.143

Intolerance Scores

LoFtool: 0.384
RVIS EVS: -0.23
RVIS percentile EVS: 36.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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