LMCD1

LIM and cysteine rich domains 1, the group of LIM domain containing

Basic information

Region (hg38): 3:8501807-8574668

Links

ENSG00000071282 ∙ NCBI:29995 ∙ OMIM:604859 ∙ HGNC:6633 ∙ Uniprot:Q9NZU5 ∙ 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 LMCD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMCD1 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		1
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in LMCD1

This is a list of pathogenic ClinVar variants found in the LMCD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-8532757-G-T		not specified	Uncertain significance (Oct 25, 2024)
3-8532765-G-C		not specified	Uncertain significance (Sep 09, 2021)
3-8532792-G-A		not specified	Uncertain significance (Jun 05, 2024)
3-8532794-A-G		not specified	Uncertain significance (Jul 09, 2021)
3-8532809-G-A		not specified	Uncertain significance (Nov 14, 2024)
3-8537252-C-T		not specified	Uncertain significance (Sep 27, 2021)
3-8537262-G-C		not specified	Uncertain significance (Aug 02, 2021)
3-8537265-G-A		not specified	Uncertain significance (Aug 05, 2024)
3-8537303-C-G		not specified	Uncertain significance (Sep 08, 2024)
3-8537303-C-T		not specified	Uncertain significance (Feb 13, 2024)
3-8537321-G-A		not specified	Uncertain significance (Dec 03, 2024)
3-8537327-C-T		not specified	Uncertain significance (Apr 20, 2023)
3-8537345-C-T		not specified	Uncertain significance (Apr 17, 2023)
3-8537407-C-T			Likely benign (Jan 01, 2023)
3-8548572-T-C		not specified	Uncertain significance (Jun 29, 2023)
3-8548606-G-T		not specified	Uncertain significance (Dec 06, 2024)
3-8548619-A-C		not specified	Uncertain significance (Dec 05, 2022)
3-8548620-C-T		not specified	Uncertain significance (Nov 07, 2023)
3-8548638-G-A		not specified	Uncertain significance (Jun 28, 2024)
3-8548640-C-T		not specified	Uncertain significance (Dec 12, 2023)
3-8548665-C-T		not specified	Uncertain significance (Jul 09, 2024)
3-8548694-C-T		not specified	Uncertain significance (Apr 27, 2023)
3-8548695-G-A		not specified	Uncertain significance (May 09, 2023)
3-8548695-G-C		not specified	Uncertain significance (May 24, 2023)
3-8548722-T-A		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMCD1	protein_coding	protein_coding	ENST00000157600	6	66413

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00118	0.990	125726	1	21	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.660	207	236	0.879	0.0000148	2372
Missense in Polyphen		72	92.19	0.781		933
Synonymous	1.28	77	92.6	0.831	0.00000614	710
Loss of Function	2.31	8	18.8	0.425	9.60e-7	210

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000112	0.0000967
Middle Eastern	0.000163	0.000163
South Asian	0.000167	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional cofactor that restricts GATA6 function by inhibiting DNA-binding, resulting in repression of GATA6 transcriptional activation of downstream target genes. Represses GATA6-mediated trans activation of lung- and cardiac tissue- specific promoters. Inhibits DNA-binding by GATA4 and GATA1 to the cTNC promoter (By similarity). Plays a critical role in the development of cardiac hypertrophy via activation of calcineurin/nuclear factor of activated T-cells signaling pathway. {ECO:0000250, ECO:0000269|PubMed:20026769}.
• Pathway: Surfactant metabolism;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.193
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.205
• hipred: Y
• hipred_score: 0.699
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lmcd1

Zebrafish Information Network

• Gene name: lmcd1
• Affected structure: atrioventricular valve
• Phenotype tag: abnormal
• Phenotype quality: functionality

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of cardiac muscle hypertrophy;cellular protein metabolic process;positive regulation of calcineurin-NFAT signaling cascade
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: transcription corepressor activity;zinc ion binding