C2orf88

chromosome 2 open reading frame 88, the group of A-kinase anchoring proteins

Basic information

Region (hg38): 2:189879609-190203484

Links

ENSG00000187699 ∙ NCBI:84281 ∙ OMIM:615117 ∙ HGNC:28191 ∙ Uniprot:Q9BSF0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C2orf88 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2orf88 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in C2orf88

This is a list of pathogenic ClinVar variants found in the C2orf88 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-190055744-G-C		Myostatin-related muscle hypertrophy	Benign (Jan 13, 2018)
2-190055808-A-G		Myostatin-related muscle hypertrophy	Benign (Jan 13, 2018)
2-190055896-T-C		Myostatin-related muscle hypertrophy	Benign (Jan 13, 2018)
2-190055926-T-C		Myostatin-related muscle hypertrophy	Benign (Jan 13, 2018)
2-190055942-G-C		Myostatin-related muscle hypertrophy	Uncertain significance (Jan 12, 2018)
2-190055985-G-A		Myostatin-related muscle hypertrophy	Uncertain significance (Jan 12, 2018)
2-190056055-C-G		Myostatin-related muscle hypertrophy	Benign (Jan 13, 2018)
2-190056112-AT-A		Myostatin-related muscle hypertrophy	Likely benign (Jun 14, 2016)
2-190056185-C-A		Myostatin-related muscle hypertrophy	Uncertain significance (Jan 13, 2018)
2-190056195-T-C		Myostatin-related muscle hypertrophy	Uncertain significance (Jan 12, 2018)
2-190056335-A-G		Myostatin-related muscle hypertrophy	Uncertain significance (Jan 13, 2018)
2-190056474-C-T		Myostatin-related muscle hypertrophy	Uncertain significance (Jan 12, 2018)
2-190056516-G-A		Myostatin-related muscle hypertrophy	Benign (Jan 13, 2018)
2-190056561-A-G		Myostatin-related muscle hypertrophy	Uncertain significance (Jan 12, 2018)
2-190056563-T-G		Myostatin-related muscle hypertrophy	Uncertain significance (Jan 13, 2018)
2-190056684-C-T		Myostatin-related muscle hypertrophy	Likely benign (Apr 27, 2017)
2-190056765-C-T		Myostatin-related muscle hypertrophy	Benign (Jan 13, 2018)
2-190056863-T-G		Myostatin-related muscle hypertrophy	Benign (Jan 13, 2018)
2-190056922-G-T		Myostatin-related muscle hypertrophy	Uncertain significance (Jan 12, 2018)
2-190056968-G-A		Myostatin-related muscle hypertrophy	Benign (Jan 12, 2018)
2-190056985-G-C		Myostatin-related muscle hypertrophy	Benign (Jan 13, 2018)
2-190056999-T-C		Myostatin-related muscle hypertrophy	Uncertain significance (Jan 12, 2018)
2-190057123-C-T		Myostatin-related muscle hypertrophy	Benign (Apr 27, 2017)
2-190057131-A-G		Myostatin-related muscle hypertrophy	Uncertain significance (Jan 12, 2018)
2-190057137-T-C		Myostatin-related muscle hypertrophy	Uncertain significance (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2orf88	protein_coding	protein_coding	ENST00000340623	1	323876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00276	0.364	124677	0	49	124726	0.000196

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0122	51	50.8	1.00	0.00000236	634
Missense in Polyphen		20	14.424	1.3866		186
Synonymous	-0.503	20	17.3	1.15	7.62e-7	167
Loss of Function	-0.892	3	1.73	1.73	7.24e-8	29

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000522	0.000522
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.0000796	0.0000795
Middle Eastern	0.000223	0.000223
South Asian	0.000588	0.000588
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to type I regulatory subunits of protein kinase A (PKA-RI) and may anchor/target them to the plasma membrane. {ECO:0000269|PubMed:23115245}.

Intolerance Scores

• loftool: 0.775
• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.94

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 1700019D03Rik

Gene ontology

• Cellular component: plasma membrane
• Molecular function: protein binding;protein kinase A regulatory subunit binding