# NM_002299.4(LCT):c.5723G>A (p.Arg1908His)

https://sugi.bio/variant/lct-p-arg1908his

## Summary

**LCT p.Arg1908His (c.5723G>A)** is classified **Uncertain significance** in LCT (ClinVar, Single submitter, 1 submitter; last evaluated 2018-09-24). AlphaMissense: likely benign (0.0674); Ultra-rare (popmax 0.0535%, eas); Associated with congenital lactase deficiency.

**At a glance:** Uncertain significance · review: Single submitter · rsID rs577825311 · 1 submitter · 1 linked condition · AlphaMissense likely benign · ultra-rare (popmax 0.0535%, eas)

## For patients & families {#patients}

This is a change in the LCT gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter, and is linked to congenital lactase deficiency.

*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.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Diagnostic panels | LCT is a diagnostic-grade gene on 7 Genomics England panels |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0012311/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [LCT](https://sugi.bio/atlas/gene/LCT/) |
| Protein change (HGVS p.) | p.Arg1908His |
| Coding change (HGVS c.) | c.5723G>A |
| MANE Select transcript | [NM_002299](https://www.ncbi.nlm.nih.gov/nuccore/NM_002299) |
| dbSNP | [rs577825311](https://www.ncbi.nlm.nih.gov/snp/rs577825311/) |
| Variant type | single nucleotide variant |
| Location | chr2:135788385-135788385 (GRCh38) |
| ClinVar | [VCV1032814](https://www.ncbi.nlm.nih.gov/clinvar/variation/1032814/) |

**All HGVS expressions:** `LRG_338:g.71785G>A`, `LRG_338t1:c.5723G>A`, `NC_000002.11:g.136545955C>T`, `NC_000002.12:g.135788385C>T`, `NG_008104.2:g.71785G>A`, `NM_002299.4:c.5723G>A`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **tolerated** — a triage signal, not a reclassification.

- AlphaMissense **likely benign** (0.0674)
- REVEL 0.035 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -7.965 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP -7.33, GERP -4.83 — fast-evolving / accelerated position
- CADD: **PHRED 0.043**. 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.*
- Regional missense constraint: **o/e 0.69** across the covering region of the MANE Select transcript (135,788,327–135,807,302), spanning 18,975 bp. Chi-square p 6.6e-18. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — this absence is genuinely unknown. Where a position sits between the lowest and the highest record the release holds for its gene, an absent score is a result and we state it as one; this position falls outside them, or the gene has no scored position at all, so that test did not reach here. It may lie outside the scored MANE transcript scope, or it may have been scored with all four deltas below Δ0.2 just past the last surviving record. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.0535%** (eas) · FAF95 0.0368% · FAF99 0.0313% · 24/44,892 in the highest group · 52/1,613,988 alleles overall — ultra-rare (popmax 0.0535%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.0535% | 1,871 |
| Admixed American | 0.005% | 19,999 |
| Remaining individuals (not grpmax-eligible) | 0.0032% | 31,243 |
| European (non-Finnish) | 0.00186% | 53,638 |
| African / African-American | 0.00134% | 74,894 |

*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}

**LCT** population constraint: LOEUF 0.62, pLI 1.7232e-11, missense-Z 4.9902; ClinGen dosage — haploinsufficiency gene assoc. with recessive phenotype, triplosensitivity 0/3. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **1908** lies in the 'required for homodimerization and transport to the plasma membrane' region.

AlphaFold model confidence (whole protein): pLDDT 86.63, 66% of residues very-high.

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

*Describes the biological roles of LCT (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:** LCT's established molecular role includes lactase activity. p.Arg1908His falls in the required for homodimerization and transport to the plasma membrane region. In Reactome, LCT is annotated in disease pathway(s) including **Intestinal saccharidase deficiencies**.

**Disease mechanism (Reactome):** LCT loss or alteration is curated in [Intestinal saccharidase deficiencies](https://reactome.org/content/detail/R-HSA-5659898).

### Pathways affected {#pathways}

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

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Intestinal saccharidase deficiencies](https://reactome.org/content/detail/R-HSA-5659898) | curated |
| [Digestion of dietary carbohydrate](https://reactome.org/content/detail/R-HSA-189085) | curated |

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

**Molecular function:** lactase activity, beta-glucosidase activity, protein homodimerization activity, phlorizin hydrolase activity.

**Biological process:** lactose catabolic process, quercetin catabolic process, cellobiose catabolic process.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2018-09-24.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Baylor Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2018-09-24 |

## Associated conditions {#conditions}

[congenital lactase deficiency](https://sugi.bio/atlas/disease/congenital-lactase-deficiency/).

**Reported phenotype names (ClinVar):** Congenital lactase deficiency, DISACCHARIDE INTOLERANCE II, ALACTASIA, CONGENITAL.

## Similar variants {#similar}

Related LCT variant pages (same residue, condition, or type): [LCT p.Arg1908Cys](/variant/lct-p-arg1908cys), [LCT p.Arg1908Ser](/variant/lct-p-arg1908ser), [LCT p.Arg1908=](/variant/lct-p-arg1908), [LCT c.4866+2T>G](/variant/lct-c-4866-plus-2t-g), [LCT p.Gln1179Ter](/variant/lct-p-gln1179ter), [LCT p.Tyr1390Ter](/variant/lct-p-tyr1390ter), [LCT c.4173+5G>A](/variant/lct-c-4173-plus-5g-a), [LCT p.Ala94Thr](/variant/lct-p-ala94thr).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); 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 2026-10-14); 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 1032814). 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.*