Is MTR p.Val1160= (c.3480C>T) pathogenic?

MTR p.Val1160= (c.3480C>T) is classified Likely benign in MTR (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-12). Ultra-rare (popmax 0.0187%, amr); Associated with methylcobalamin deficiency type cblG.

What condition is associated with MTR p.Val1160= (c.3480C>T)?

MTR p.Val1160= (c.3480C>T) is associated with methylcobalamin deficiency type cblG (ClinVar).

How common is MTR p.Val1160= (c.3480C>T) in the general population?

MTR p.Val1160= (c.3480C>T) is ultra-rare (popmax 0.0187%, amr) (gnomAD).

How is Homocystinuria without methylmalonic aciduria inherited?

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

MTR p.Val1160=

c.3480C>T · rs776477351 · VCV2740040

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0187%, amr)

Conditions

methylcobalamin deficiency type cblG

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -6.1	GERP -3.4
Overall
CADD	1.267	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0187% Admixed American · 11/58,852 alleles

Filtering AF 0.0104% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00809%

Overall 0.00131% 21/1,603,018 alleles · ultra-rare exomes 14/1,450,824 · genomes 7/152,194 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0187%	5,350
East Asian	0.0112%	8,912
Remaining individualsnot grpmax-eligible	0.00161%	62,002
Finnishnot grpmax-eligible	0.00158%	63,148
African / African-American	0.00134%	74,780
European (non-Finnish)	0.00017%	587,278

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: MTR
Protein: p.Val1160=
Coding: c.3480C>T
MANE Select: NM_000254
dbSNP: rs776477351
Type: single nucleotide variant
Location: chr1:236895432 (GRCh38)
Gene constraint: LOEUF 0.625 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 87.60 · 9 PDB
Residue 1160: an α-helix; the adomet activation domain

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

Disease context

methylcobalamin deficiency type cblG — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Homocystinuria without methylmalonic aciduria (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages

Similar variants

MTR p.Val1160Ile Uncertain significance ★ ⚠ same residue
MTR c.1812+1G>A Likely pathogenic ★★ same condition
MTR c.2474-1G>C Pathogenic ★★ same condition
MTR c.2595-2A>G Likely pathogenic ★★ same condition
MTR c.340-166A>G Pathogenic/Likely pathogenic ★★ same condition
MTR c.609+1088G>A Pathogenic ★★ same condition
MTR c.866-2A>C Pathogenic/Likely pathogenic ★★ same condition
MTR p.Arg1147Ter Pathogenic ★★ 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/mtr-p-val1160 (accessed [today's date]).

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