HNRNPD

heterogeneous nuclear ribonucleoprotein D, the group of Heterogeneous nuclear ribonucleoproteins|RNA binding motif containing

Basic information

Region (hg38): 4:82352498-82374503

Previous symbols: [ "AUF1", "HNRPD" ]

Links

ENSG00000138668 ∙ NCBI:3184 ∙ OMIM:601324 ∙ HGNC:5036 ∙ Uniprot:Q14103 ∙ 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 HNRNPD gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPD 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						0
missense			19			19
nonsense		1				1
start loss						0
frameshift	1		1			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					7	7
Total	1	1	20	0	7

Highest pathogenic variant AF is 0.00000659

Variants in HNRNPD

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

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

Position	Type	Phenotype	Significance	ClinVar
4-82355233-G-A			Benign (Jun 19, 2021)
4-82355277-C-CA			Benign (Jun 19, 2021)
4-82355394-C-G		not specified	Uncertain significance (May 01, 2024)
4-82356594-A-C		not specified	Uncertain significance (Jan 03, 2024)
4-82356609-G-C		not specified	Uncertain significance (Jun 01, 2023)
4-82356647-T-C		not specified	Uncertain significance (Dec 28, 2022)
4-82356801-C-G		not specified	Uncertain significance (Apr 17, 2023)
4-82356847-G-A		Neurodevelopmental disorder	Likely pathogenic (Jul 17, 2023)
4-82356853-G-A		Intellectual disability	Likely pathogenic (May 06, 2024)
4-82356863-T-C		HNRNPD-related disorder	Likely benign (Feb 24, 2020)
4-82357329-T-C		not specified	Uncertain significance (Sep 26, 2024)
4-82357363-G-A		not specified	Uncertain significance (Aug 30, 2021)
4-82357375-T-C		not specified	Uncertain significance (May 01, 2024)
4-82357407-T-C		not specified	Uncertain significance (Dec 12, 2022)
4-82357408-T-G		not specified	Uncertain significance (Jan 30, 2025)
4-82357416-T-C		not specified	Uncertain significance (Aug 28, 2024)
4-82357427-G-GAGCT			Uncertain significance (Jul 01, 2018)
4-82357625-T-C			Benign (Jun 19, 2021)
4-82357762-T-A			Benign (Jun 19, 2021)
4-82358569-T-C			Benign (Jun 19, 2021)
4-82358578-C-T			Benign (Jun 19, 2021)
4-82358670-C-T		not specified	Uncertain significance (Dec 02, 2024)
4-82359487-G-A		not specified	Uncertain significance (Apr 10, 2025)
4-82371537-C-T		not specified	Uncertain significance (Jan 09, 2025)
4-82371559-A-AGT		Intellectual disability	Likely pathogenic (Jul 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HNRNPD	protein_coding	protein_coding	ENST00000313899	8	22006

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00379	125738	0	4	125742	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.45	91	185	0.492	0.00000885	2316
Missense in Polyphen		16	69.378	0.23062		890
Synonymous	1.48	50	65.1	0.768	0.00000342	648
Loss of Function	4.03	1	20.9	0.0479	0.00000106	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto- oncogenes and cytokine mRNAs. Also binds to double- and single- stranded DNA sequences in a specific manner and functions a transcription factor. Each of the RNA-binding domains specifically can bind solely to a single-stranded non-monotonous 5'-UUAG-3' sequence and also weaker to the single-stranded 5'-TTAGGG-3' telomeric DNA repeat. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'- TTAGGG-3' repeats. Binding of RRM1 to DNA inhibits the formation of DNA quadruplex structure which may play a role in telomere elongation. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. May play a role in the regulation of the rhythmic expression of circadian clock core genes. Directly binds to the 3'UTR of CRY1 mRNA and induces CRY1 rhythmic translation. May also be involved in the regulation of PER2 translation. {ECO:0000269|PubMed:10080887, ECO:0000269|PubMed:11051545, ECO:0000269|PubMed:24423872}.
• Pathway: mRNA Processing;AUF1 (hnRNP D0) binds and destabilizes mRNA;Metabolism of RNA;mRNA Splicing - Major Pathway;Regulation of mRNA stability by proteins that bind AU-rich elements;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.426

Intolerance Scores

• loftool: 0.160
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.212
• hipred: Y
• hipred_score: 0.783
• ghis: 0.724

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hnrnpd
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; immune system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: mRNA splicing, via spliceosome;liver development;regulation of transcription, DNA-templated;RNA processing;RNA catabolic process;RNA metabolic process;cerebellum development;regulation of telomere maintenance;regulation of circadian rhythm;regulation of mRNA stability;positive regulation of translation;positive regulation of transcription, DNA-templated;mRNA stabilization;response to calcium ion;response to electrical stimulus;3'-UTR-mediated mRNA destabilization;cellular response to amino acid stimulus;cellular response to estradiol stimulus;cellular response to nitric oxide;circadian regulation of translation;response to rapamycin;positive regulation of telomere capping;response to sodium phosphate;cellular response to putrescine;positive regulation of telomerase RNA reverse transcriptase activity;hepatocyte dedifferentiation
• Cellular component: nucleus;nucleoplasm;cytosol;synapse;ribonucleoprotein complex
• Molecular function: AT DNA binding;chromatin binding;RNA binding;mRNA binding;protein binding;transcription factor binding;mRNA 3'-UTR AU-rich region binding;telomeric DNA binding;histone deacetylase binding;sequence-specific DNA binding;sequence-specific double-stranded DNA binding