C2orf42

chromosome 2 open reading frame 42

Basic information

Region (hg38): 2:70149884-70248615

Links

ENSG00000115998 ∙ NCBI:54980 ∙ ∙ HGNC:26056 ∙ Uniprot:Q9NWW7 ∙ 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 C2orf42 gene.

• Inborn genetic diseases (5 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2orf42 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in C2orf42

This is a list of pathogenic ClinVar variants found in the C2orf42 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-70150427-A-G		not specified	Uncertain significance (Nov 12, 2021)
2-70150447-C-T		not specified	Uncertain significance (Jul 26, 2021)
2-70160694-C-T		not specified	Uncertain significance (Sep 09, 2021)
2-70165163-C-G		not specified	Uncertain significance (Sep 27, 2021)
2-70179608-G-C		not specified	Uncertain significance (Sep 30, 2021)
2-70181459-G-A		not specified	Uncertain significance (Nov 06, 2015)
2-70212723-T-G		Welander distal myopathy	Uncertain significance (May 10, 2022)
2-70212723-TG-T		Welander distal myopathy	Uncertain significance (Sep 04, 2016)
2-70212730-C-T		Welander distal myopathy	Pathogenic (Dec 15, 2023)
2-70212734-C-A		Welander distal myopathy	Likely benign (Aug 31, 2022)
2-70212739-C-T		Amyotrophic lateral sclerosis 26 with or without frontotemporal dementia • Welander distal myopathy	Uncertain significance (Jan 22, 2024)
2-70212758-C-T		Welander distal myopathy	Benign/Likely benign (Jan 28, 2024)
2-70212762-T-C		Welander distal myopathy	Uncertain significance (Jul 05, 2022)
2-70212763-T-C		Welander distal myopathy	Uncertain significance (Oct 13, 2023)
2-70212772-T-C		Welander distal myopathy	Uncertain significance (Apr 28, 2023)
2-70212779-A-G		Welander distal myopathy	Benign (Nov 27, 2023)
2-70212779-A-AT		Welander distal myopathy	Uncertain significance (Jul 25, 2022)
2-70212784-G-A		Welander distal myopathy	Uncertain significance (Sep 13, 2019)
2-70212794-C-T		not specified • Welander distal myopathy	Benign/Likely benign (Jan 26, 2024)
2-70212795-G-A		AMYOTROPHIC LATERAL SCLEROSIS 26 WITH FRONTOTEMPORAL DEMENTIA • Welander distal myopathy	Conflicting classifications of pathogenicity (Dec 06, 2023)
2-70212798-T-G		Welander distal myopathy	Uncertain significance (Nov 30, 2022)
2-70212802-C-T		Welander distal myopathy	Uncertain significance (Jan 20, 2024)
2-70212808-A-C		Welander distal myopathy	Uncertain significance (Jul 15, 2022)
2-70212810-T-C		Welander distal myopathy • not specified • TIA1-related disorder • Amyotrophic lateral sclerosis 26 with or without frontotemporal dementia	Conflicting classifications of pathogenicity (Apr 01, 2024)
2-70212821-C-A		Welander distal myopathy	Uncertain significance (Sep 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2orf42	protein_coding	protein_coding	ENST00000264434	8	98736

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00514	0.995	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	267	321	0.833	0.0000179	3725
Missense in Polyphen		81	105.3	0.76922		1158
Synonymous	1.29	106	124	0.853	0.00000650	1156
Loss of Function	3.23	9	27.2	0.331	0.00000149	311

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000298	0.000297
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000109	0.000109
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.250
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.46

Haploinsufficiency Scores

• pHI: 0.216
• hipred: N
• hipred_score: 0.476
• ghis: 0.477

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: C87436

Gene ontology

• Cellular component: nucleus;nuclear membrane
• Molecular function: protein binding