Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_001130987.2(DYSF):c.3114G>A (p.Pro1038=)

CA222150

94299 (ClinVar)

Gene: DYSF (HGNC:8291)

Condition: autosomal recessive limb-girdle muscular dystrophy (MONDO:0015152)

Inheritance Mode: Autosomal recessive inheritance

UUID: 9e5bf7d2-f973-4ada-b086-7cb8c9e3f36a

Approved on: 2026-01-23

Published on: 2026-02-17

HGVS expressions

NM_001130987.2(DYSF):c.3114G>A (p.Pro1038=)

NM_001130987.2:c.3114G>A

NC_000002.12:g.71570627G>A

CM000664.2:g.71570627G>A

NC_000002.11:g.71797757G>A

CM000664.1:g.71797757G>A

NC_000002.10:g.71651265G>A

NG_008694.1:g.122005G>A

ENST00000698057.1:c.486G>A

ENST00000258104.8:c.3060G>A

ENST00000410020.8:c.3114G>A

ENST00000258104.7:c.3060G>A

ENST00000394120.6:c.3063G>A

ENST00000409366.5:c.3063G>A

ENST00000409582.7:c.3111G>A

ENST00000409651.5:c.3156G>A

ENST00000409744.5:c.3021G>A

ENST00000409762.5:c.3111G>A

ENST00000410020.7:c.3114G>A

ENST00000410041.1:c.3114G>A

ENST00000413539.6:c.3153G>A

ENST00000429174.6:c.3060G>A

ENST00000461565.1:n.226G>A

NM_001130455.1:c.3063G>A

NM_001130976.1:c.3018G>A

NM_001130977.1:c.3018G>A

NM_001130978.1:c.3060G>A

NM_001130979.1:c.3153G>A

NM_001130980.1:c.3111G>A

NM_001130981.1:c.3111G>A

NM_001130982.1:c.3156G>A

NM_001130983.1:c.3063G>A

NM_001130984.1:c.3021G>A

NM_001130985.1:c.3114G>A

NM_001130986.1:c.3021G>A

NM_001130987.1:c.3114G>A

NM_003494.3:c.3060G>A

NM_001130455.2:c.3063G>A

NM_001130976.2:c.3018G>A

NM_001130977.2:c.3018G>A

NM_001130978.2:c.3060G>A

NM_001130979.2:c.3153G>A

NM_001130980.2:c.3111G>A

NM_001130981.2:c.3111G>A

NM_001130982.2:c.3156G>A

NM_001130983.2:c.3063G>A

NM_001130984.2:c.3021G>A

NM_001130985.2:c.3114G>A

NM_001130986.2:c.3021G>A

NM_003494.4:c.3060G>A

Likely Benign

BS1

BP7 BP4 PM3

Evidence Links 0

Expert Panel

Limb Girdle Muscular Dystrophy VCEP

Criteria Specification Information

Criteria Specification: ClinGen Limb Girdle Muscular Dystrophy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DYSF Version 2.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Limb Girdle Muscular Dystrophy VCEP

The NM_003494.4: c.3060G>A p.(Pro1020=) variant in DYSF, which is also known as NM_001130987.2: c.3114G>A p.(Pro1038=), is a synonymous (silent) variant that is not located in a splice region (outside of the first and the last 3 bases of the exon). This variant was detected in a heterozygous state in one individual with suspected LGMD and disease range dysferlin expression. This individual also had two additional variants in DYSF in unknown phase (PM3 and BP2 not met; PMID: 30564623, LOVD Individual #00222264; Jain Foundation Dysferlin Registry internal data communication). The filtering allele frequency for this variant is 0.001555 in gnomAD v4.1.0 (the lower threshold of the 95% CI of 162/91072 South Asian chromosomes), which is higher than the VCEP threshold of 0.001 (BS1). The SpliceAI prediction score for this variant is 0.17, which is greater than the VCEP threshold of <0.05 (BP4 not met). In summary, this variant meets the criteria to be classified as Likely Benign for autosomal recessive limb girdle muscular dystrophy based on the ACMG/AMP criteria applied, as specified by the ClinGen LGMD VCEP (specifications v2.0.0; 01/23/2026): BS1.

BS1

The filtering allele frequency for this variant is 0.001555 in gnomAD v4.1.0 (the lower threshold of the 95% CI of 162/91072 South Asian chromosomes), which is higher than the VCEP threshold of 0.001 (BS1).

BP7

The SpliceAI prediction score for this variant is 0.17, which is greater than the VCEP threshold of <0.05 (BP4 not met). Per VCEP, BP4 needs to be met to apply BP7.

BP4

The SpliceAI prediction score for this variant is 0.17, which is greater than the VCEP threshold of <0.05 (BP4 not met).

PM3

This variant was detected in a heterozygous state in one individual with suspected LGMD and disease range dysferlin expression. This individual also had two additional variants in DYSF in unknown phase (PM3 and BP2 not met; PMID: 30564623, LOVD Individual #00222264; Jain Foundation Dysferlin Registry internal data communication).

Curation History

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