ANKRD49

protein-coding

ankyrin repeat domain 49, the group of Ankyrin repeat domain containing

Gene summary

Involved in positive regulation of DNA-templated transcription. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_017704.3

Inheritance

—

ClinVar variants

U:14B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr11:94,493,979-94,499,578

External References & Databases

Ensembl (ENSG00000168876)

Transcript & Mutation Effects

hg38 • Region Span ~5.6 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 ANKRD49 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 14

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017704.3. 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						0
missense			13 clinvar	2 clinvar		15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	14	2	0	16

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017704.3	RefSeq	NP_060174.2	2	MANE Select
ENST00000544612.6	Ensembl	ENSP00000440396.1	2	MANE Select
ENST00000302755.4	Ensembl	ENSP00000303518.3	2	Standard
ENST00000302755.5	Ensembl	ENSP00000303518.3	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatogenesis
cell differentiation
positive regulation of transcription, DNA-templated

Molecular Function

protein binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000544612
Coding exons: 2
Length: 5955
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125747
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.887	99	127	0.779	0.00000630	1589
Missense (PolyPhen)		24	31.875	0.75294		413
Synonymous	1.32	36	47.6	0.757	0.00000242	446
Loss of Function	0.869	6	8.78	0.684	5.04e-7	98

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00018	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Induces HBG1 expression (PubMed:16131492, PubMed:11162141). May have a role in spermatogenesis where it promotes autophagy in response to serum starvation, via the NF- kappaB pathway (By similarity). {ECO:0000250|UniProtKB:Q8VE42, ECO:0000269|PubMed:11162141, ECO:0000269|PubMed:16131492}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.731
RVIS EVS: -0.23
RVIS percentile EVS: 36.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.147

Gene Damage Prediction

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