Is LMTK1 p.Pro795Ser (c.2383C>T) pathogenic?

LMTK1 p.Pro795Ser (c.2383C>T) is classified Likely benign in LMTK1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-03). AlphaMissense: likely benign (0.071); Ultra-rare (popmax 0.0298%, nfe).

How common is LMTK1 p.Pro795Ser (c.2383C>T) in the general population?

LMTK1 p.Pro795Ser (c.2383C>T) is ultra-rare (popmax 0.0298%, nfe) (gnomAD).

What do computational predictors say about LMTK1 p.Pro795Ser (c.2383C>T)?

AlphaMissense predicts likely benign (score 0.071) — an in-silico prediction, not a clinical call.

LMTK1 p.Pro795Ser

c.2383C>T · rs377469093 · VCV2373418

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.071 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0298%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.071	likely benign
REVEL	0.167	moderately benign-leaning
SaProt	LLR -6.53	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.55 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.72	GERP -2.6, phastCons 0.003
Regional constraint	o/e 1.22	unconstrained · MANE · 4,291 bp · p 2.4e-16 · regional, not allelic
Overall
CADD	6.713	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0298% European (non-Finnish) · 339/1,137,060 alleles

Filtering AF 0.0272% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0262%

Overall 0.0238% 364/1,528,274 alleles · ultra-rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0358%	2,796
European (non-Finnish)grpmax	0.0298%	3,354
African / African-American	0.00413%	24,189
Finnishnot grpmax-eligible	0.00172%	58,090

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: LMTK1
Protein: p.Pro795Ser
Coding: c.2383C>T
MANE Select: NM_001080395
dbSNP: rs377469093
Type: single nucleotide variant
Location: chr17:81121553 (GRCh38)
Gene constraint: LOEUF 1.574 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 48.54
Residue 795: the 'disordered' region

Full LMTK1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

LMTK1 p.Ala1020Asp Uncertain significance ★ same type
LMTK1 p.Ala1153Ser Uncertain significance ★ same type
LMTK1 p.Ala1191Val Uncertain significance ★ same type
LMTK1 p.Ala1204Val Uncertain significance ★ same type
LMTK1 p.Ala1367Asp Uncertain significance ★ same type
LMTK1 p.Ala1374Ser Uncertain significance ★ same type
LMTK1 p.Ala193Thr Uncertain significance ★ same type
LMTK1 p.Ala21Thr 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/lmtk1-p-pro795ser (accessed [today's date]).

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