MAP7D2

MAP7 domain containing 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): X:20006713-20116907

Links

ENSG00000184368 ∙ NCBI:256714 ∙ ∙ HGNC:25899 ∙ Uniprot:Q96T17 ∙ 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 MAP7D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP7D2 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			45	5		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	45	5	1

Variants in MAP7D2

This is a list of pathogenic ClinVar variants found in the MAP7D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-20010875-G-A			Benign (Nov 20, 2018)
X-20010951-C-T		not specified	Uncertain significance (Oct 14, 2023)
X-20010970-T-C		not specified	Uncertain significance (Mar 22, 2024)
X-20010987-C-G		not specified	Uncertain significance (Oct 20, 2021)
X-20010990-G-A		not specified	Uncertain significance (Dec 19, 2022)
X-20011021-G-C		not specified	Uncertain significance (Feb 15, 2023)
X-20011024-T-G		not specified	Uncertain significance (Feb 02, 2022)
X-20012352-A-T		not specified	Uncertain significance (May 02, 2024)
X-20012356-C-T		not specified	Uncertain significance (Aug 28, 2023)
X-20012470-G-A		not specified	Uncertain significance (Jan 11, 2023)
X-20012482-G-C		not specified	Uncertain significance (Feb 17, 2024)
X-20015266-T-C		not specified	Uncertain significance (Apr 06, 2023)
X-20015281-C-T		not specified	Uncertain significance (Mar 25, 2024)
X-20015282-G-T		not specified	Uncertain significance (Apr 19, 2023)
X-20015302-C-T		not specified	Likely benign (Sep 14, 2023)
X-20015303-G-C		not specified	Uncertain significance (Feb 27, 2024)
X-20015312-T-C		not specified	Likely benign (Apr 20, 2024)
X-20016108-T-C		not specified	Uncertain significance (Apr 29, 2024)
X-20016170-C-T		not specified	Likely benign (May 03, 2023)
X-20016207-C-T		not specified	Uncertain significance (Mar 29, 2023)
X-20016237-G-A		not specified	Uncertain significance (Apr 01, 2024)
X-20016278-C-T		not specified	Uncertain significance (Feb 27, 2024)
X-20025023-T-C		not specified	Uncertain significance (Sep 28, 2021)
X-20025026-G-C		not specified	Uncertain significance (Feb 23, 2023)
X-20025050-G-A		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP7D2	protein_coding	protein_coding	ENST00000379643	16	110205

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0414	0.959	125713	17	18	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.246	306	294	1.04	0.0000235	4963
Missense in Polyphen		93	91.272	1.0189		1433
Synonymous	-0.354	115	110	1.04	0.00000861	1520
Loss of Function	3.85	9	32.8	0.274	0.00000281	527

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000150	0.000135
Ashkenazi Jewish	0.000135	0.0000992
East Asian	0.000144	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000323	0.000229
Middle Eastern	0.000144	0.000109
South Asian	0.000161	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.282
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.69

Haploinsufficiency Scores

• pHI: 0.271
• hipred: N
• hipred_score: 0.273
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map7d2
• Phenotype: normal phenotype

Gene ontology

• Biological process: microtubule cytoskeleton organization
• Cellular component: microtubule cytoskeleton