Is LCT p.Asp106= (c.318C>T) pathogenic?

LCT p.Asp106= (c.318C>T) is classified Benign/Likely benign in LCT (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-02-01). Common (popmax 6.81%, amr) — too common for a highly-penetrant pathogenic allele; Associated with congenital lactase deficiency.

What condition is associated with LCT p.Asp106= (c.318C>T)?

LCT p.Asp106= (c.318C>T) is associated with congenital lactase deficiency (ClinVar).

How is Congenital lactase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

LCT p.Asp106=

Q: How common is LCT p.Asp106= (c.318C>T) in the general population?

LCT p.Asp106= (c.318C>T) is common (popmax 6.81%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.318C>T · rs34307240 · VCV331213

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 6.81%, amr) — too common for a highly-penetrant pathogenic allele

Conditions

congenital lactase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.55	GERP -3.5
Overall
CADD	4.613	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.81% Admixed American · 4,085/60,006 alleles

Filtering AF 6.63% ClinGen BA1/BS1 input FAF95, joint · FAF99 6.56%

Overall 0.922% 14,875/1,614,134 alleles · common

Ancestry group	Frequency	1 in
Admixed Americangrpmax	6.81%	15
Amishnot grpmax-eligible	1.43%	70
Middle Eastern	1.42%	70
South Asian	1.27%	79
Ashkenazi Jewishnot grpmax-eligible	0.865%	116
Remaining individualsnot grpmax-eligible	0.853%	117
Finnishnot grpmax-eligible	0.8%	125
European (non-Finnish)	0.683%	146
African / African-American	0.237%	422
East Asian	0.00446%	22,442

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: LCT
Protein: p.Asp106=
Coding: c.318C>T
MANE Select: NM_002299
dbSNP: rs34307240
Type: single nucleotide variant
Location: chr2:135836852 (GRCh38)
Gene constraint: LOEUF 0.62 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.63
Residue 106: the 'glycosyl hydrolase-1 1; region i' region

Full LCT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

congenital lactase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Congenital lactase deficiency (Orphanet):

Inheritance: Autosomal recessive

Similar variants

LCT p.Asp106Glu Uncertain significance ★★ ⚠ same residue
LCT c.4866+2T>G Likely pathogenic ★★ same condition
LCT p.Gln1179Ter Pathogenic/Likely pathogenic ★★ same condition
LCT p.Tyr1390Ter Pathogenic ★★ same condition
LCT c.4173+5G>A Uncertain significance ★★ same condition
LCT p.Ala94Thr Uncertain significance ★★ ⚠ same condition
LCT p.Gln594Glu Uncertain significance ★★ ⚠ same condition
LCT p.Gly1400Ser Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/lct-p-asp106 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown