LRRC75A

leucine rich repeat containing 75A

Basic information

Region (hg38): 17:16441576-16492193

Previous symbols: [ "C17orf76", "FAM211A" ]

Links

ENSG00000181350 ∙ NCBI:388341 ∙ ∙ HGNC:32403 ∙ Uniprot:Q8NAA5 ∙ 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 LRRC75A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC75A 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				4		4
missense			18	2	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	6	1

Variants in LRRC75A

This is a list of pathogenic ClinVar variants found in the LRRC75A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-16443644-C-T		not specified	Uncertain significance (Sep 29, 2023)
17-16443686-C-T		not specified	Uncertain significance (May 24, 2023)
17-16443766-C-T		not specified	Uncertain significance (Jan 23, 2023)
17-16443866-T-C		not specified	Uncertain significance (Oct 13, 2023)
17-16443894-G-T		not specified	Likely benign (Feb 13, 2024)
17-16443901-C-T		not specified	Uncertain significance (May 02, 2024)
17-16443931-C-T			Benign (Dec 20, 2017)
17-16443936-C-T		not specified	Likely benign (Dec 16, 2023)
17-16444060-C-T		not specified	Uncertain significance (Jul 13, 2021)
17-16444065-G-A		not specified	Likely benign (May 24, 2023)
17-16444100-C-T		not specified	Uncertain significance (Dec 14, 2022)
17-16444102-G-T		not specified	Uncertain significance (Jun 07, 2023)
17-16447876-G-A		not specified	Uncertain significance (Mar 29, 2022)
17-16447923-C-T		not specified	Uncertain significance (Feb 26, 2024)
17-16447942-C-T		not specified	Likely benign (Mar 27, 2023)
17-16447957-C-T		not specified	Uncertain significance (Nov 17, 2023)
17-16462272-G-A		not specified	Uncertain significance (Jan 26, 2023)
17-16462303-G-A			Likely benign (Aug 01, 2022)
17-16462328-C-T		not specified	Uncertain significance (May 26, 2023)
17-16491839-T-C		not specified	Uncertain significance (Jan 16, 2024)
17-16491849-T-G		not specified	Likely benign (Apr 07, 2023)
17-16491878-C-G		not specified	Uncertain significance (Dec 15, 2023)
17-16491923-C-T		not specified	Uncertain significance (Feb 07, 2023)
17-16491939-C-T		not specified	Uncertain significance (Apr 09, 2024)
17-16491955-C-G		not specified	Uncertain significance (May 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC75A	protein_coding	protein_coding	ENST00000470794	4	50577

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.696	0.301	125181	0	4	125185	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	141	183	0.769	0.0000120	2159
Missense in Polyphen		79	108.48	0.72827		1131
Synonymous	-0.944	92	81.2	1.13	0.00000513	781
Loss of Function	2.33	1	8.20	0.122	4.36e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000184	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.66

Haploinsufficiency Scores

• pHI: 0.228
• hipred: N
• hipred_score: 0.386

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Lrrc75a

Gene ontology

• Cellular component: cytoplasm