Is LRTOMT p.Ser68= (c.204C>T) pathogenic?

LRTOMT p.Ser68= (c.204C>T) is classified Likely benign in LRTOMT (ClinVar, Single submitter, 1 submitter; last evaluated 2016-11-13). Very rare (popmax 0.00137%, afr).

How common is LRTOMT p.Ser68= (c.204C>T) in the general population?

LRTOMT p.Ser68= (c.204C>T) is very rare (popmax 0.00137%, afr) (gnomAD).

LRTOMT p.Ser68=

c.204C>T · rs890009722 · VCV505397

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00137%, afr)

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 0.89	GERP -0.39, phastCons 0.45
Overall
CADD	8.797	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00137% African / African-American · 1/73,056 alleles

Overall 0.000129% 2/1,550,764 alleles · very rare exomes 1/1,398,554 · genomes 1/152,210 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00137%	73,056
European (non-Finnish)	8.72e-05%	1,146,988

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: LRTOMT
Protein: p.Ser68=
Coding: c.204C>T
dbSNP: rs890009722
Type: single nucleotide variant
Location: chr11:72106056 (GRCh38)
Gene constraint: LOEUF 1.315 · pLI <0.01 (gnomAD)

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

Similar variants

LRTOMT p.Ser68fs Likely pathogenic ★ same residue
LRTOMT c.358+4A>C Pathogenic/Likely pathogenic ★★ same type
LRTOMT p.Arg81Gln Pathogenic/Likely pathogenic ★★ same type
ANAPC15 p.Pro99Leu Uncertain significance ★★ ⚠ same type
LRTOMT c.-123T>C Uncertain significance ★★ same type
LRTOMT c.-254G>T Uncertain significance ★★ same type
LRTOMT c.*1488T>G Uncertain significance ★★ same type
LRTOMT p.Arg52Gln Uncertain significance ★★ ⚠ same type

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/lrtomt-p-ser68 (accessed [today's date]).

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