LY6G6F

protein-coding

lymphocyte antigen 6 family member G6F, the group of V-set domain containing|LY6/PLAUR domain containing

Gene summary

The human G6f protein is a type I transmembrane protein belonging to the immunoglobin (Ig) superfamily, which is comprised of cell-surface proteins involved in the immune system and cellular recognition (de Vet et al., 2003 [PubMed 12852788]).[supplied by OMIM, Mar 2008]

Previous symbols:

LY6G6D
C6orf21

MANE transcript

NM_001003693.3

Inheritance

—

ClinVar variants

U:44B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr6:31,706,866-31,710,679

External References & Databases

Ensembl (ENSG00000204424)

Transcript & Mutation Effects

hg38 • Region Span ~3.8 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 LY6G6F variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 45

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001003693.3. 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						0
missense			43 clinvar	2 clinvar	1 clinvar	46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	44	2	1	47

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001003693.3	RefSeq	NP_001003693.1	6	MANE Select
ENST00000375832.5	Ensembl	ENSP00000364992.5	6	MANE Select
ENST00001098527.1	Ensembl	ENSP00000768333.1	5	Standard
ENST00001135070.1	Ensembl	ENSP00000810599.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Platelet degranulation
Response to elevated platelet cytosolic Ca2+
Platelet activation, signaling and aggregation
Hemostasis

Biological Process

platelet degranulation

Cellular Component

plasma membrane
integral component of membrane
platelet alpha granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375832
Coding exons: 6
Length: 10942
Individuals with no LoFs: 125643
Homozygous LoFs: 0
Heterozygous LoFs: 104
Defined: 125747
p: 0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.677	147	172	0.855	0.00000935	1896
Missense (PolyPhen)		29	34.104	0.85035		356
Synonymous	1.08	59	70.5	0.837	0.00000400	630
Loss of Function	0.873	11	14.6	0.753	7.10e-7	153

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00052	0.00052	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00047	0.00047	rare
South Asian	0.00065	0.00065	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in the downstream signal transduction pathways involving GRB2 and GRB7. {ECO:0000269|PubMed:12852788}.;

Recessive Scores

pRec: 0.0865

Intolerance Scores

LoFtool: 0.798
RVIS EVS: 1.33
RVIS percentile EVS: 94.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.518

Gene Damage Prediction

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