CFHR2

complement factor H related 2, the group of Complement system regulators and receptors|Sushi domain containing

Basic information

Region (hg38): 1:196943738-196959622

Previous symbols: [ "HFL3", "CFHL2" ]

Links

ENSG00000080910 ∙ NCBI:3080 ∙ OMIM:600889 ∙ HGNC:4890 ∙ Uniprot:P36980 ∙ 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 CFHR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFHR2 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				1	3	4
missense			11	7	2	20
nonsense				1		1
start loss						0
frameshift			1		1	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1	11	12
Total	0	0	12	10	17

Variants in CFHR2

This is a list of pathogenic ClinVar variants found in the CFHR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-196943816-C-G			Benign (Jun 19, 2021)
1-196943898-TG-T			Uncertain significance (May 23, 2023)
1-196943911-T-C			Uncertain significance (Sep 26, 2022)
1-196944067-C-G			Benign (Jun 18, 2021)
1-196949443-T-C		not specified	Likely benign (Oct 20, 2023)
1-196949462-C-G		not specified	Uncertain significance (Jul 12, 2022)
1-196949475-A-G		not specified	Conflicting classifications of pathogenicity (Oct 10, 2023)
1-196949510-A-G		not specified	Benign (Aug 10, 2023)
1-196949591-C-A			Likely benign (Dec 19, 2018)
1-196949602-G-T		not specified	Likely benign (Aug 10, 2023)
1-196949604-A-G			Uncertain significance (Jan 30, 2023)
1-196949608-C-T		Atypical hemolytic-uremic syndrome	Likely benign (Jul 01, 2024)
1-196949609-G-A		Atypical hemolytic-uremic syndrome	Benign (Jul 08, 2022)
1-196949611-G-A		Atypical hemolytic-uremic syndrome	Benign (Jul 08, 2022)
1-196949613-G-A		not specified	Conflicting classifications of pathogenicity (Apr 19, 2023)
1-196949662-C-T			Likely benign (-)
1-196950846-C-G		not specified	Likely benign (Apr 03, 2024)
1-196950923-A-G		Kidney disorder	Benign/Likely benign (Apr 01, 2023)
1-196950926-G-A		not specified	Uncertain significance (Mar 29, 2023)
1-196950930-AAATT-A			Benign (Dec 31, 2019)
1-196950942-A-T		not specified	Uncertain significance (Jun 07, 2023)
1-196950964-C-G		not specified	Uncertain significance (Mar 24, 2023)
1-196950990-A-G		not specified	Uncertain significance (Apr 24, 2023)
1-196950993-G-A			Benign (Dec 31, 2019)
1-196951018-C-T			Benign (Nov 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFHR2	protein_coding	protein_coding	ENST00000367415	5	139459

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.51e-8	0.0640	125302	4	428	125734	0.00172

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.902	160	131	1.22	0.00000607	1734
Missense in Polyphen		65	52.265	1.2437		643
Synonymous	-2.21	64	45.1	1.42	0.00000211	502
Loss of Function	-0.535	11	9.24	1.19	3.88e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.0190	0.0189
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0190	0.0189
South Asian	0.00238	0.00235
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in complement regulation. The dimerized forms have avidity for tissue-bound complement fragments and efficiently compete with the physiological complement inhibitor CFH. Can associate with lipoproteins and may play a role in lipid metabolism. {ECO:0000269|PubMed:23487775}.
• Pathway: Human Complement System;Innate Immune System;Immune System;Regulation of Complement cascade;Complement cascade (Consensus)

Recessive Scores

• pRec: 0.0924

Intolerance Scores

• loftool: 0.687
• rvis_EVS: 1.35
• rvis_percentile_EVS: 94.31

Haploinsufficiency Scores

• pHI: 0.0447
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0767

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of complement activation;negative regulation of protein binding;positive regulation of cytolysis
• Cellular component: extracellular region;protein-containing complex
• Molecular function: protein binding;protein homodimerization activity;protein heterodimerization activity