Is INMT p.Ter264Ser (c.791G>C) pathogenic?

INMT p.Ter264Ser (c.791G>C) is classified Benign in INMT (ClinVar, Single submitter, 1 submitter; last evaluated 2016-03-29). Low-frequency (popmax 3.43%, nfe).

How common is INMT p.Ter264Ser (c.791G>C) in the general population?

INMT p.Ter264Ser (c.791G>C) is low-frequency (popmax 3.43%, nfe) (gnomAD).

INMT p.Ter264Ser

c.791G>C · rs61741736 · VCV402980

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

stop-loss

predicted LoF

gnomAD v4.1

Rare

low-frequency (popmax 3.43%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	stop-loss	predicted loss-of-function
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.8	GERP -0.58, phastCons 0.31
Overall
CADD	8.956	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.43% European (non-Finnish) · 40,295/1,174,428 alleles

Filtering AF 3.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.39%

Overall 2.89% 46,347/1,604,138 alleles · low-frequency exomes 43,062/1,451,802 · genomes 3,285/152,336 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	3.43%	29
Finnishnot grpmax-eligible	3.23%	31
Remaining individualsnot grpmax-eligible	2.5%	40
South Asian	1.49%	67
Admixed American	1.09%	92
Middle Eastern	0.929%	108
African / African-American	0.551%	181
Amishnot grpmax-eligible	0.219%	456
Ashkenazi Jewishnot grpmax-eligible	0.13%	772
East Asian	0.0112%	8,942

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: INMT
Protein: p.Ter264Ser
Coding: c.791G>C
MANE Select: NM_006774
dbSNP: rs61741736
Type: single nucleotide variant
Location: chr7:30755850 (GRCh38)
Gene constraint: LOEUF 1.467 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 97.14 · 1 PDB

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

Similar variants

INMT c.363-7T>A Likely benign ★★ same type
INMT p.Ala104Thr Uncertain significance ★ ⚠ same type
INMT p.Ala134Glu Uncertain significance ★ ⚠ same type
INMT p.Ala215Thr Uncertain significance ★ ⚠ same type
INMT p.Ala247Ser Uncertain significance ★ ⚠ same type
INMT p.Ala247Val Uncertain significance ★ ⚠ same type
INMT p.Arg137Trp Uncertain significance ★ ⚠ same type
INMT p.Arg177His 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/inmt-p-ter264ser (accessed [today's date]).

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