ETFRF1

electron transfer flavoprotein regulatory factor 1, the group of LYR motif containing

Basic information

Region (hg38): 12:25195216-25209645

Previous symbols: [ "LYRM5" ]

Links

ENSG00000205707 ∙ NCBI:144363 ∙ ∙ HGNC:27052 ∙ Uniprot:Q6IPR1 ∙ 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 ETFRF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ETFRF1 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 ETFRF1

This is a list of pathogenic ClinVar variants found in the ETFRF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-25204207-T-G		not specified	Uncertain significance (Oct 12, 2021)
12-25205273-C-T		Noonan syndrome	Uncertain significance (Jun 14, 2016)
12-25205297-A-G		Noonan syndrome	Conflicting classifications of pathogenicity (May 01, 2022)
12-25205312-C-T		Noonan syndrome	Uncertain significance (Jun 14, 2016)
12-25205367-C-G		Noonan syndrome	Conflicting classifications of pathogenicity (Jun 01, 2023)
12-25205484-T-C		Noonan syndrome	Likely benign (Jun 14, 2016)
12-25205488-C-CAA		Noonan syndrome	Likely benign (Jun 14, 2016)
12-25205716-A-T		Noonan syndrome • Noonan syndrome and Noonan-related syndrome	Benign/Likely benign (Dec 23, 2020)
12-25205721-C-T		Noonan syndrome	Uncertain significance (Jun 14, 2016)
12-25205728-CT-C		Cardio-facio-cutaneous syndrome • Noonan syndrome	Conflicting classifications of pathogenicity (Aug 01, 2022)
12-25205728-CTT-C		Cardio-facio-cutaneous syndrome • Noonan syndrome	Likely benign (Jun 14, 2016)
12-25205736-T-C			Likely benign (Dec 01, 2022)
12-25205880-T-C		Noonan syndrome	Conflicting classifications of pathogenicity (Oct 01, 2022)
12-25205894-T-G		Noonan syndrome	Likely benign (Jun 14, 2016)
12-25206009-T-C		Noonan syndrome	Likely benign (Jun 14, 2016)
12-25206035-T-G		Noonan syndrome	Likely benign (Jun 14, 2016)
12-25206037-CAGAT-C		Cardio-facio-cutaneous syndrome • Noonan syndrome	Uncertain significance (Jun 14, 2016)
12-25206111-G-GA		Cardio-facio-cutaneous syndrome • Noonan syndrome	Likely benign (Jun 14, 2016)
12-25206111-G-GAA		Cardio-facio-cutaneous syndrome • Noonan syndrome	Uncertain significance (Jun 14, 2016)
12-25206150-T-C		Noonan syndrome	Conflicting classifications of pathogenicity (May 01, 2023)
12-25206244-G-C		Noonan syndrome	Conflicting classifications of pathogenicity (Jul 01, 2022)
12-25206293-A-T		Noonan syndrome	Likely benign (Jun 14, 2016)
12-25206296-G-A		Noonan syndrome	Uncertain significance (Jun 14, 2016)
12-25206341-A-G		Noonan syndrome	Uncertain significance (Jun 14, 2016)
12-25206394-A-T		Noonan syndrome	Likely benign (Jun 14, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ETFRF1	protein_coding	protein_coding	ENST00000381356	2	14430

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000108	0.0578	124493	0	22	124515	0.0000883

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.428	49	41.3	1.19	0.00000214	581
Missense in Polyphen		17	14.107	1.2051		192
Synonymous	0.201	13	14.0	0.932	6.82e-7	154
Loss of Function	-1.88	7	3.31	2.12	2.25e-7	52

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000330	0.000322
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000120	0.000115
Middle Eastern	0.00	0.00
South Asian	0.000108	0.0000981
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a regulator of the electron transfer flavoprotein by promoting the removal of flavin from the ETF holoenzyme (composed of ETFA and ETFB). {ECO:0000269|PubMed:27499296}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.398
• ghis: 0.590

Mouse Genome Informatics

• Gene name: Etfrf1

Gene ontology

• Biological process: respiratory electron transport chain
• Cellular component: mitochondrion
• Molecular function: protein binding