MAP7D1

protein-coding

MAP7 domain containing 1

Gene summary

Predicted to be involved in microtubule cytoskeleton organization. Located in spindle. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

PARCC1
RPRC1

MANE transcript

NM_001388490.1

Inheritance

—

ClinVar variants

U:155B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr1:36,155,579-36,180,849

External References & Databases

Ensembl (ENSG00000116871)

Transcript & Mutation Effects

hg38 • Region Span ~25.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAP7D1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 147

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001388490.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	1 clinvar	3
missense			150 clinvar	4 clinvar	2 clinvar	156
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	155	6	3	164

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001388490.1	RefSeq	NP_001375419.1	17	MANE Select
ENST00000474796.2	Ensembl	ENSP00000507044.1	17	MANE Select
NM_001286365.2	RefSeq	NP_001273294.1	16	Standard
NM_001286366.2	RefSeq	NP_001273295.1	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule cytoskeleton organization

Cellular Component

spindle
cytosol
microtubule cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373151
Coding exons: 17
Length: 25271
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125745
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.00	449	513	0.876	0.0000351	5240
Missense (PolyPhen)		169	187.76	0.90011		1804
Synonymous	0.491	193	202	0.956	0.0000129	1771
Loss of Function	5.06	6	40.9	0.147	0.00000227	471

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000058	0.000054	rare
Finnish	0.000049	0.000046	rare
European (Non-Finnish)	0.000021	0.000018	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0910

Intolerance Scores

LoFtool: 0.472
RVIS EVS: -0.33
RVIS percentile EVS: 30.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.607

Gene Damage Prediction

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