# NM_001148.6(ANK2):c.1803T>C (p.His601=)

https://sugi.bio/variant/ank2-p-his601

## Summary

**ANK2 p.His601= (c.1803T>C)** is classified **Benign/Likely benign** in ANK2 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2024-04-22). Very rare (popmax 0.00267%, afr); Associated with long QT syndrome.

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs144016063 · 5 submitters · 2 linked conditions · very rare (popmax 0.00267%, afr)

## For patients & families {#patients}

This is a change in the ANK2 gene that is classified as benign/likely benign — not considered disease-causing, submitted by 5 submitters, and is linked to long QT syndrome.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Clinical trials | 68 registered for this condition — see ClinicalTrials.gov |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0027044/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [ANK2](https://sugi.bio/atlas/gene/ANK2/) |
| Protein change (HGVS p.) | p.His601= |
| Coding change (HGVS c.) | c.1803T>C |
| MANE Select transcript | [NM_001148](https://www.ncbi.nlm.nih.gov/nuccore/NM_001148) |
| dbSNP | [rs144016063](https://www.ncbi.nlm.nih.gov/snp/rs144016063/) |
| Variant type | single nucleotide variant |
| Location | chr4:113278480-113278480 (GRCh38) |
| ClinVar | [VCV413959](https://www.ncbi.nlm.nih.gov/clinvar/variation/413959/) |

**All HGVS expressions:** `LRG_327:g.465398T>C`, `LRG_327t1:c.1803T>C`, `NC_000004.11:g.114199636T>C`, `NC_000004.12:g.113278480T>C`, `NG_009006.2:g.465398T>C`, `NM_001127493.3:c.1740T>C`, `NM_001148.6:c.1803T>C`, `NM_001354225.2:c.1803T>C`, `NM_001354228.2:c.1803T>C`, `NM_001354230.2:c.1848T>C`, `NM_001354231.2:c.1848T>C`, `NM_001354232.2:c.1803T>C`, `NM_001354235.2:c.1803T>C`, `NM_001354236.2:c.1803T>C`, `NM_001354237.2:c.1848T>C`, `NM_001354239.2:c.1740T>C`, `NM_001354240.2:c.1848T>C`, `NM_001354241.2:c.1848T>C`, `NM_001354242.2:c.1848T>C`, `NM_001354243.2:c.1740T>C`, `NM_001354244.2:c.1740T>C`, `NM_001354245.2:c.1782+545T>C`, `NM_001354246.2:c.1803T>C`, `NM_001354249.2:c.1716T>C`, `NM_001354252.2:c.1740T>C`, `NM_001354253.2:c.1719+545T>C`, `NM_001354254.2:c.1740T>C`, `NM_001354255.2:c.1740T>C`, `NM_001354256.2:c.1740T>C`, `NM_001354257.2:c.1719+545T>C`, `NM_001354258.2:c.1803T>C`, `NM_001354260.2:c.1695+545T>C`, `NM_001354261.2:c.1761T>C`, `NM_001354262.2:c.1740T>C`, `NM_001354264.2:c.1716T>C`, `NM_001354265.2:c.1803T>C`, `NM_001354266.2:c.1716T>C`, `NM_001354267.2:c.1716T>C`, `NM_001354268.2:c.1782+545T>C`, `NM_001354269.3:c.1593T>C`, `NM_001354270.2:c.1719+545T>C`, `NM_001354271.2:c.1695+545T>C`, `NM_001354272.2:c.1740T>C`, `NM_001354273.2:c.1605T>C`, `NM_001354274.2:c.1716T>C`, `NM_001354275.2:c.1740T>C`, `NM_001354276.2:c.1716T>C`, `NM_001354277.2:c.1518T>C`, `NM_001386142.1:c.1716T>C`, `NM_001386143.1:c.1740T>C`, `NM_001386144.1:c.1848T>C`, `NM_001386146.1:c.1716T>C`, `NM_001386147.1:c.1761T>C`, `NM_001386148.2:c.1791T>C`, `NM_001386149.1:c.1716T>C`, `NM_001386150.1:c.1716T>C`, `NM_001386151.1:c.1695+545T>C`, `NM_001386152.1:c.1848T>C`, `NM_001386153.1:c.1716T>C`, `NM_001386154.1:c.1716T>C`, `NM_001386156.1:c.1719+545T>C`, `NM_001386157.1:c.1518T>C`, `NM_001386158.1:c.1497+545T>C`, `NM_001386160.1:c.1761T>C`, `NM_001386161.1:c.1740T>C`, `NM_001386162.1:c.1716T>C`, `NM_001386174.1:c.1854T>C`, `NM_001386175.1:c.1830T>C`, `NM_001386186.2:c.1791T>C`, `NM_001386187.2:c.1767T>C`, `NM_020977.5:c.1803T>C`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 0.078, GERP -4.03, phastCons 0.974 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 8.222**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **below the reporting threshold**. This position is scored for a different substitution (T>G, Δ0.75 acceptor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.00267%** (afr) · FAF95 0.000443% · FAF99 0.000166% · 2/74,902 in the highest group · 3/1,613,876 alleles overall — very rare (popmax 0.00267%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 0.00267% | 37,451 |
| European (non-Finnish) | 8.48e-05% | 1,179,935 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**ANK2** population constraint: LOEUF 0.271, pLI 1, missense-Z 4.2752; ClinGen dosage — haploinsufficiency 3, triplosensitivity 0 (0–3 scale). *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **complex neurodevelopmental disorder** — Definitive (AD)
- **Brugada syndrome** — Disputed (AD)
- **catecholaminergic polymorphic ventricular tachycardia** — Disputed (AD)
- **long QT syndrome** — Disputed (AD)

## Protein context {#protein}

Residue **601** lies in an α-helix.

**11 experimental structure(s)** (PDB): [4D8O](https://www.rcsb.org/structure/4D8O), [4RLV](https://www.rcsb.org/structure/4RLV), [4RLY](https://www.rcsb.org/structure/4RLY), [5Y4D](https://www.rcsb.org/structure/5Y4D), [5Y4E](https://www.rcsb.org/structure/5Y4E), [5Y4F](https://www.rcsb.org/structure/5Y4F).

## What this gene does {#gene-function}

*Describes the biological roles of ANK2 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** ANK2's established molecular role includes enzyme binding.


### Pathways affected {#pathways}

ANK2 participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [COPI-mediated anterograde transport](https://reactome.org/content/detail/R-HSA-6807878) | curated |
| [Interaction between L1 and Ankyrins](https://reactome.org/content/detail/R-HSA-445095) | electronic |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** enzyme binding, protein kinase binding, spectrin binding, transmembrane transporter binding, phosphorylation-dependent protein binding.

**Biological process:** regulation of heart rate, atrial septum development, intracellular protein localization, positive regulation of gene expression, regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion, regulation of cardiac muscle contraction by calcium ion signaling.

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2024-04-22.

**Submitter consensus:** conflicting (3 Likely benign, 2 Benign).

**Submission history:** 5 submissions (2015–2024); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2024-04-22 |
| Genome-Nilou Lab | Benign | criteria provided, single submitter | clinical testing | 2021-12-05 |
| GeneDx | Benign | criteria provided, single submitter | clinical testing | 2015-03-03 |
| Ambry Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2019-11-21 |
| PreventionGenetics, part of Exact Sciences | Likely benign | no assertion criteria provided | clinical testing | 2019-07-03 |

## Associated conditions {#conditions}

[long QT syndrome](https://sugi.bio/atlas/disease/long-qt-syndrome/), [cardiac arrhythmia, ankyrin-B-related](https://sugi.bio/atlas/disease/cardiac-arrhythmia-ankyrin-b-related/).

**Reported phenotype names (ClinVar):** Long QT syndrome, Cardiac arrhythmia, ankyrin-B-related, not provided, Cardiovascular phenotype, ANK2-related disorder, ANKYRIN-B SYNDROME, ANK2-related condition, none provided.

## Similar variants {#similar}

Related ANK2 variant pages (same residue, condition, or type): [ANK2 p.His601Asn](/variant/ank2-p-his601asn), [ANK2 p.His601Arg](/variant/ank2-p-his601arg), [ANK2 p.His601Gln](/variant/ank2-p-his601gln), [ANK2 p.Arg1007Ter](/variant/ank2-p-arg1007ter), [ANK2 p.Arg1088Ter](/variant/ank2-p-arg1088ter), [ANK2 p.Arg3113Ter](/variant/ank2-p-arg3113ter), [ANK2 c.11032+11G>T](/variant/ank2-c-11032-plus-11g-t), [ANK2 c.11611-3T>A](/variant/ank2-c-11611-minus-3t-a).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 413959). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*